The document details the development of a bioinformatics system called Mitochondriome-Exome Wide Associations (MEWAS) for studying the relationships between mitochondrial DNA and nuclear exomes in physiological and pathological phenotypes. It discusses the importance of mitochondria in cellular functions, the impact of mitochondrial DNA mutations on various diseases, and the integration of mitochondrial and nuclear genomic data for research. Additionally, it outlines the computational strategies used in MEWAS to analyze data from the 1000 Genomes Project and highlights contributions from various academic professionals.

1. Mitochondriome-Exome Wide Associations (MEWAs):
sviluppo di un sistema bioinformatico per studi di associazione fra
l'intero esoma nucleare e il DNA mitocondriale
in fenotipi fisiologici e patologici
Maria Angela Diroma
Università degli Studi di Bari - Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica

2. Mitochondriome-Exome Wide Associations
(MEWAs)
MToolBox

3. ...the importance of being a mitochondrion
ü cellular power plants
ü signaling through mitochondrial
reactive oxygen species
ü regulation of the membrane potential
ü control of the cell cycle and cell
growth
ü motility
ü cellular differentiation
ü apoptosis-programmed cell death
ü storage of calcium ions and calcium
signaling
ü synthesis of aminoacids, haem,
nucleotides and lipids

4. …the double face of mtDNA mutations
‘Classical’ mtDNA diseases:
•
•
•
•
LHON (Leber Hereditary
Optic Neuropathy)
MERFF (Myoclonic Epilepsy
with Ragged Red Fibers)
MELAS (Mitochondrial
encephalomyopathy)
KSS (Kearns–Sayre
syndrome)
Other disorders:
•
•
•
•
•
•
Parkinson’s disease
Alzheimer’s disease
Type 2 Diabetes
Deafness
Multiple Sclerosis
Cancer …
Human evolution and
phylogeny

5. Haplogroup: group of mtDNA
haplotypes derived by descent from
the same ancestral mtDNA molecule as
revealed by the sharing of a
distinguishing mutational motif
Torroni et al. 2006, Harvesting the fruit of the human
mtDNA tree. TRENDS in Genetics, 22(6)
RSRS: Reconstructed Sapiens Reference Sequence
Behar et al. 2012, A “Copernican” reassessment of the human
mitochondrial DNA tree from its root. Am. J of Human Genetics 90,
675-684

6. HmtDB
Human mitochondrial DataBase
Since 2005 HmtDB supports
population genetics and biomedical
research
Currently it includes 14144 and 1612
complete human mitochondrial
sequences from healthy and patients,
respectively

7. ü The Query function allows the user to
retrieve data from the database
!
example of a genome card
ü The downloading function allows to
download
o multialignments of the entire
healthy and pathologic as well as
of the continent specific datasets
o variability data obtained by
applying SiteVar and MitVarProt
software
ü The application of the classify
procedure allows the prediction of
the haplogroup on the basis of the
classification available through
Phylotree (build R15).
o comparison of a query genome
with the reference sequence RSRS,
based on the application of the
MUSCLE software
o a genome card of the submitted
genome is generated and
displayed

8. mt-classifier
ü Haplogroup prediction of the genome
(either complete or incomplete) based on
Phylotree Build 15
ü Functional annotation of each variant site
by comparing the query genome with the
related hg_MARGe (haplogroup Major
Allele Reference Genome) sequence
ü Identification of private mutations of the
genome
Santorsola et al. 2013, The mitochondrial Major Allele Reference
Genome (MARGe): a tool to isolate functionally relevant
mutations in human mitochondrial sequences. Under review

9. NumtS: Nuclear mitochondrial Sequence
190 Human NumtS
41 validated by PCR
766 NumtS
(585 assembled NumtS)
Similarity: 63-100%
ü NumtS and their mitochondrial counterparts
evolve at different rates
ü NumtS insertion is an ongoing process
outgroups for population genetics
NumtS tracks useful for studies
concerning
ü human structural variation
ü diversity
ü disease

10. Integration of information from both
mitochondrial and nuclear genomes may
favour
ü molecular evolution studies
ü clinical studies
Mitochondriome-Exome Wide Associations
(MEWAs)
Whole Exome Sequencing (WES)
• high depth of coverage with relatively few reads
• cost-effective
• faster
ü overlapping of nuclear probes
onto NumtS
ü stoichiometric ratios between
nuclear and mitochondrial
molecules
Association among
• mitochondrial variants
• nuclear exome variants
• phenotype data

11. MEWAs pipeline
Overview of the early computational strategy by
Picardi and Pesole
Application of the pipeline to more
than 1200 healthy samples from the
1000 Genomes Project revealed a
widespread population occurrence of
rare events predicted to be damaging
Diroma et al. 2013, Extraction and annotation of
human mitochondrial genomes from 1000 Genomes
Whole Exome Sequencing data. Under review
ü WES reads alignment onto reference genomes
• RSRS (mitochondrial genome)
• hg19 (nuclear genome)
ü NumtS filtering
ü Mitochondrial DNA assembly
ü Haplogroup prediction
ü Functional annotation and prioritization of
mitochondrial and nuclear variants
ü Statistical analyses to support association
between nuclear and mitochondrial variants to a
specific phenotype

12. Acknowledgments
Prof. Marcella Attimonelli, University of Bari
Prof. Graziano Pesole, IBBE / University of Bari
Prof. Maria Svelto, University of Bari
Prof. Marni Falk, CHOP / University of Pennsylvania
Prof. Giorgio Pietro Maggi, INFN / Politecnico of Bari
Prof. Stefano Maria Pagnotta, University of Sannio
Ernesto Picardi, IBBE / University of Bari
Giuseppe Gasparre, University of Bologna
Giacinto Donvito, INFN
Domenico Simone, IBBE / University of Milano
Mariangela Santorsola, University of Sannio
Claudia Calabrese, University of Bologna
Cristiano Guttà, University of Bari
Francesco Maria Calabrese, University of Napoli
Dario Leonardo Balacco, University of Nottingham

13. Thanks for your attention