Tag: sift

Stan vs PyMC3 vs Bean Machine

I have been a light user of Stan and RStan for some time and while there are a lot of things I really like about the language (such as the awesome community you can turn to for support and ShinyStan for inspecting Stan output) there are also a few things…

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Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

Significance Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids…

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Ethnic Diversity of DPD activity and the DPYD Gene

Plain Language Summary Fluoropyrimidine (FP; 5-FU, capecitabine) is a common chemotherapy used to treat many different cancers, including cancer of the colon and rectum, upper digestive tract, breast and head and neck. Cancer patients who receive FP chemotherapy are at risk of developing severe side effects from their treatment. A…

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Disease Causing Mutations Databases or database for predicting the functional consiquence of the mutation

Disease Causing Mutations Databases or database for predicting the functional consiquence of the mutation 1 I would like to analyze the functional consequence of the mutation in the protein-coding region of the human genome like in TP53 or EGFR etc. I tried Annovar, VEP, SIFT, polyphen, etc but as far…

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Mammoth-elephant hybrids could be created within the decade. Should they be?

The park’s vision of bringing back ancient grasslands is “an exciting hypothesis,” says University of Maine palaeoecologist Jacquelyn Gill, based on the effects that today’s elephants have on their habitats. However, she cautions that researchers still don’t know the full details of how woolly mammoths’ ecosystems functioned, which complicates efforts…

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Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Significance The collection of large amounts of whole-genome sequencing data allowed for identification of mutational signatures, which are characteristic combinations of substitutions in the context of neighboring bases. The clinical significance of these mutational signatures is still largely unknown. In neuroblastoma, we showed that high levels of cytosine > adenine…

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VEP plugin uses

VEP plugin uses 0 It is a small question, I downloaded all plugins and wrote in the input script to get plugin experimental functionalities (I am using merged cache Ref_Seq & Ensembl both). # make a file with a single variant using bash echo “17 43071077 43071077 T/C + variant_1″…

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Interpreting dbNSFP prediction scores

Interpreting dbNSFP prediction scores 1 How should I interpret for example, SIFT score: SIFT_pred = T;T;T;T;D;T SIFT_score = 0.138;0.138;0.138;0.138;0.042;0.157 From dbNSFP documentation, I understand the meaning of D and T D: Deleterious (sift<=0.05); T: tolerated (sift>0.05) My question is: Why there are multiple values of both pred and score in…

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Need suggestions about pathogenicity prediction of gdc level 3 SNV file

Hi, I am trying to figure out which tool is most accurate in terms of pathogenicity prediction of TCGA SNVs level 3 data. TCGA offers SIFT, PolyPhen, and IMPACT scores for different kinds of mutations. SIFT, and PolyPhen cover mainly “Missense Mutation”, while IMPACT categorizes every kind of mutation into…

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Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

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