Whole genome analyses reveal no pathogenetic single nucleotide or structural differences between monozygotic twins discordant for amyotrophic lateral sclerosis

Abstract

The contribution of genetic and environmental factors to the pathogenesis of sporadic amyotrophic lateral sclerosis (ALS) remains unclear. To investigate the genetic component of the disease, we performed whole genome sequencing on ALS discordant monozygotic twins. Illumina whole genome sequencing on white blood cell DNA of five ALS-discordant monozygotic twin pairs (10 samples in total) yielded ∼30x coverage per individual. All single nucleotide variants, indels, and structural variants (copy number variants, inversions and translocations) were called and evaluated for functional consequence, evolutionary conservation, population frequency and overlap with known ALS associated variants and genes. Results showed that no validated discordant coding or regulatory single nucleotide variants or indels were found, and nor were any genome-wide discordant structural variants detected. Concordant variants of particular interest were: 1) two rare, highly-conserved heterozygous non-synonymous variants in SYT9 and EWSR1, genes previously associated with ALS (out of 2044 rare heterozygous variants detected); 2) three rare homozygous missense variants; and 3) three novel copy number deletions that overlapped genes. In conclusion, no convincing coding or regulatory nucleotide or genome-wide structural differences were found between ALS discordant monozygotic twins. The results suggest that more work is needed to elucidate possible environmental, epigenetic, oligogenic and somatic genetic factors that could underlie susceptibility to sporadic ALS.

Key words::

• Amyotrophic lateral sclerosis
• motor neuron disease
• monozygotic twin study
• whole genome sequencing
• gene variant
• genetics
• genomics

Acknowledgements

We thank ALS patients and their twin siblings for donating DNA samples, treating neurologists for supplying clinical information, and MND Associations in all Australian states for assisting with sample collections. At the University of Sydney, Ronald Trent provided laboratory facilities, Pak Leng Cheong undertook the C9orf72 mutation testing, and Stephen Kum Jew provided technical assistance. At the Genome Institute at Washington University, the Production and Apipe groups contributed to the study, Joanne Nelson assisted with the dbGaP submission, Shelly O’Laughlin, Elizabeth Appelbaum and Catrina Fronick undertook sample processing and sequencing, Gabriel Sanderson provided bioinformatic support, Bob Fulton and Lucinda Fulton were project managers, and Heather Schmidt undertook manual reviews and 3730 validations.

The study was supported by an Australian National Health and Medical Research Council Project Grant #1032443, the Motor Neuron Disease Research Institute of Australia, and the Aimee Stacey and Ignacy Burnett bequests. Blood DNA samples were obtained from the Australian Motor Neuron Disease DNA Bank which is supported by an Australian National Health and Research Council Enabling Grant #402703.

Declaration of interest: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Supplementary material available online

Supplementary Tables 1–9.