Precision HLA typing from next-generation sequencing data

Authors: András Szolek, Benjamin Schubert, Christopher Mohr
Date: April 2014
Version: 1.0
License: OptiType is released under a three-clause BSD license

OptiType, is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all minor and major HLA-I alleles.

OptiType uses the following software and libraries:

1. Python 2.7
2. Biopython 1.63
3. Coopr 3.3
4. Matplotlib 1.3.1
5. Pandas 0.12 (with HDF5 support)
6. HDF5 1.8.11
7. RazerS 3.1
8. Cplex 12.5

Please make sure you have installed said software/libraries and their dependencies.

First install all required software and libraries and register the static path in the configuration file for RazerS 3.1. CPLEX should be globally executable via command line. Alternative ILP solver supported by Cooper are also usable. Please do not change the folder structure or make sure you changed the necessary entries in the config file.

1. First filter the read files with the following settings:

>razers3 --percent-identity 90 --max-hits 1 --distance-range 0 --output-format sam --output sample_fished.sam
         ./data/hla_reference.fasta sample.fastq

where reference.fasta is either nuc_reference.fasta or gen_reference.fasta depending on the type of NGS data. The references can be found in the ./data sub-folder or in the supplementary material. To use the results as input for OptiType the sam-files have to be converted into fastq format. On Unix- based operating system you can convert from sam to fastq with the following command:

>cat sample_fished.sam | grep -v ^@ | awk '{print "@"$1"\n"$10"\n+\n"$11}' > sample_fished.fastq

For paired-end data pre-process each file individually.

2. After pre-filtering, OptiType can be called as follows:

>python OptiTypePipeline.py -i sample_fished_1.fastq [sample_fished_2.fastq]
                    (--rna | --dna) [--beta BETA] [--enumerate ENUMERATE]
                    --o ./out_dir/

This will produce a CSV with the optimal typing and possible sub-optimal typings if specified, as well as a coverage plot of the genotype for diagnostic purposes and a HTML file containing a summary of the results.

>python OptiTypePipeline.py --help  
usage: OptiType [-h] --input INPUT [INPUT ...] (--rna | --dna) [--beta BETA]  
                [--enumerate ENUMERATE] --outdir OUTDIR [--verbose]

OptiType: 4-digit HLA typer

optional arguments:
  -h, --help            show this help message and exit
  --input INPUT [INPUT ...], -i INPUT [INPUT ...]
                        Fastq files with fished HLA reads. Max two files (for
                        paired-end)
  --rna, -r             Specifiying the mapped data as RNA.
  --dna, -d             Specifiying the mapped data as DNA.
  --beta BETA, -b BETA  The beta value for for homozygosity detection.
  --enumerate ENUMERATE, -e ENUMERATE
                        The number of enumerations.
  --outdir OUTDIR, -o   OUTDIR
                        Specifies the out directory to which all files should
                        be written
  --verbose, -v         Set verbose mode on.

DNA data (paired-end):

python OptiTypePipeline.py -i ./test/exome/NA11995_SRR766010_1_fished.fastq ./test/exome/NA11995_SRR766010_2_fished.fastq -d -v -o ./test/exome/

RNA data (paired-end):

python OptiTypePipeline.py -i ./test/rna/CRC_81_N_2_fished.fastq ./test/rna/CRC_81_N_2_fished.fastq -r -v -o ./test/rna/

András Szolek
szolek@informatik.uni-tuebingen.de
University of Tübingen, Applied Bioinformatics,
Center for Bioinformatics, Quantitative Biology Center,
and Dept. of Computer Science,
Sand 14, 72076 Tübingen, Germany

1. http://python.org/download/
2. http://biopython.org/
3. http://software.sandia.gov/trac/coopr
4. http://matplotlib.org/
5. http://pandas.pydata.org/
6. http://www.hdfgroup.org/HDF5/
7. https://www.seqan.de/projects/razers/
8. http://www-01.ibm.com/software/info/ilog/

Szolek, A., Schubert, B., Mohr, C., Feldhahn, M., Strum, M., & Kohlbacher, O. (2014). OptiType: precision HLA typing from next-generation sequencing data. (in review)