MitoPathoPy

Search for potential pathological mutations in your human mtDNA sequence
Author: Edvard Ehler, PhD (edvard.ehler@img.cas.cz)
Year: 2020

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This tool will search for the (potential) pathological mutations in you mtDNA samples. To get the right input format, please, use the Haplogrep 2 (https://haplogrep.i-med.ac.at/app/index.html) tool to turn your sequences (fastas) into HSD format file. Haplogrep can be also downloaded and run localy (https://github.com/seppinho/haplogrep-cmd). Pathological mtDNA mutations are taken from data published at https://www.mitomap.org/MITOMAP.

HSD format is a simple, tab delimited text file with 4 or more columns. Here are the examples taken from Haplogrep GitHub and their online test data:

ID	 Range	 Haplogroup	 Polymorphisms
Sample1	1-16569	?	263G	315.1C	750G	1041G	1438G	4769G	8860G	9410G	12358G	13656C	15326G	16189C	16192T	16519C
Sample2 1-16569 H100 263G 315.1C 750G 1041G 1438G 4769G 8860G 9410G 12358G 13656C 15326G 16189C 16192T 16519C
Sample3 1-16569 ? 73G 263G 315.1C 750G 1438G 3010A 3107C 4769G 5111T 8860G 10257T 12358G 15326G 16145A 16222T 16519C
Sample4	16024-16569;1-576;2092;3552;4071;4491;4833;4883;8414;8473;9090;9824;10397;10400;11959;11969;12372;12771;13563;14502;14569;15487;	G2a1d	73G	260A	263G	309.1C	315.1C	489C	4833G	10400T	13563G	14569A	16183C	16189C	16193.1C	16223T	16278T	16362C
Sample5	16024-16569;1-576;1119;1719;1736;3547;3970;4820;5417;8277;8281-8289;8392;9123;10310;10398;11914;12007;12338;12358;12705;12714;14502;15535;	B4h	73G	263G	309.1CC	315.1C	523d	524d	8281d	8282d	8283d	8284d	8285d	8286d	8287d	8288d	8289d	16129A	16182C	16183C	16189C	16217C	16261T	16319A	16497G 

Workflow

1. Prepare your samples into HSD format.

2. With mitopatho.py and mitopatho_db_v1.pickle in you directory run:
   mitopatho.py -i your_input.hsd -o output.txt or potentialy python mitopatho.py -i your_input.hsd -o output.txt
   You will need just Python 3.6 (and up) with installed Pandas (v. 1.0.3 and up should work).

3. The output file is tab separated file, one line per sample, following format:

    sample_name   allele1,disease1,status1;allele2,disease2,status2;allele3,disease3,status3;...
   

We also invite you to check our Ancient mtDNA Database where you will find sequencies, metadata and also the pathologies of ancient human mtDNA samples at: https://amtdb.org/.

If you use this tool in you research, please, consider citing our article:
Ehler E, Novotný J, Juras A, Chyleński M, Moravčík O, Pačes J. AmtDB: a database of ancient human mitochondrial genomes. Nucleic acids research. 2019 Jan 8;47(D1):D29-32. https://academic.oup.com/nar/article-abstract/47/D1/D29/5106144