recipe t1dgrs2

Generate a Type 1 Diabetes Genetic Risk Score (T1D GRS) that accounts for interactions between HLA DR-DQ risk haplotypes.

Homepage:

https://github.com/t2diabetesgenes/t1dgrs2

License:

GPL / GPLv3

Recipe:

/t1dgrs2/meta.yaml

An improved T1D GRS (by Sharp et al., 2019) that incorporates both non-HLA and HLA risk components in discriminating between cases and controls, by accounting for interactions between HLA DR-DQ haplotype combinations. This uses 67 T1D-associated variants in either GRCh37 or GRCh38 to perform both a linear scoring of the genetic risk, with the added HLA DR-DQ interaction effect for the final GRS.

This Python package can be used on both imputed genotyping array and next generation sequencing (e.g., whole genome sequencing) input datasets, but will require quality control procedures to be applied beforehand.

Required: PLINK 1.9 fileset (.bed, .bim, .fam).

Please download all configuration files under the 'data' directory from the [Github page](https://github.com/t2diabetesgenes/t1dgrs2) and adjust paths in 't1dgrs2_setttings.yml' accordingly.

### Authors * Diane P Fraser ([email](mailto:d.p.fraser@exeter.ac.uk)) * Seth A Sharp ([email](mailto:ssharp@stanford.edu)) * Ankit M Arni ([email](mailto:a.m.arni@exeter.ac.uk)) * Richard A Oram ([email](mailto:r.oram@exeter.ac.uk)) * Michael N Weedon ([email](mailto:m.n.weedon@exeter.ac.uk)) * Kashyap A Patel ([email](mailto:k.a.patel@exeter.ac.uk))

### References 1. Oram RA, Patel K, Hill A, et al. (2016) A Type 1 Diabetes Genetic Risk Score Can Aid Discrimination Between Type 1 and Type 2 Diabetes in Young Adults. Diabetes Care 39(3): 337-344. [10.2337/dc15-1111](https://doi.org/10.2337/dc15-1111). 2. Patel KA, Oram RA, Flanagan SE, et al. (2016) Type 1 Diabetes Genetic Risk Score: A Novel Tool to Discriminate Monogenic and Type 1 Diabetes. Diabetes 65(7): 2094-2099. [10.2337/db15-1690](https://doi.org/10.2337/db15-1690). 3. Sharp SA, Rich SS, Wood AR, et al. (2019) Development and Standardization of an Improved Type 1 Diabetes Genetic Risk Score for Use in Newborn Screening and Incident Diagnosis. Diabetes Care 42(2): 200-207. [10.2337/dc18-1785](https://doi.org/10.2337/dc18-1785).

package t1dgrs2

(downloads) docker_t1dgrs2

versions:

0.1.2-0,  0.1.1-0,  0.1.0-0

depends numpy:

1.24.*

depends pandas:

1.5.*

depends plink:

depends python:

>=3.11

depends pyyaml:

6.0.*

depends scipy:

1.10.*

depends setuptools:

67.6.*

depends wheel:

0.40.*

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install t1dgrs2

and update with::

   mamba update t1dgrs2

To create a new environment, run:

mamba create --name myenvname t1dgrs2

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/t1dgrs2:<tag>

(see `t1dgrs2/tags`_ for valid values for ``<tag>``)

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