Rare variant analyses validate known ALS genes in a multi-ethnic population and identifies ANTXR2 as a candidate in PLS
Authors: Pottinger Tess D. , Motelow Joshua E. , Povysil Gundula , Moreno Cristiane A. Martins , Ren Zhong , Phatnani Hemali , Harms Matthew B. , Kwan Justin , Sareen Dhruv , Wang Han-I. , Broach James R. , Simmons Zachary , Arcila-Londono Ximena , Parrott Steve , Lee Edward B. , Parrott Steve , Deerlin Vivianna M. Van , Fraenkel Ernest , Ostrow Lyle W. , Baas Frank , Zaitlen Noah , Berry James D. , Malaspina Andrea , Fratta Pietro , Cox Gregory A. , Thompson Leslie M. , Finkbeiner Steve , Dardiotis Efthimios , Miller Timothy M. , Chandran Siddharthan , Parrott Steve , Pal Suvankar , Hornstein Eran , MacGowan Daniel J. , Heiman-Patterson Terry , Hammell Molly G. , Patsopoulos Nikolaos A. , Dubnau Joshua , Nath Avindra , Aitman Timothy J. , Santoyo-Lopez Javier , Williams Nicola , Berg Jonathan , McGowan Ruth , Miedzybrodzka Zosia , Porteous Mary , Tobias Edward , Mitsumoto Hiroshi , Factor-Litvak Pam , Santella Regina , Andrews Howard , Heitzman Daragh , Bedlack Richard S. , Katz Jonathan S. , Miller Robert , Parrott Steve , Forshew Dallas , Barohn Richard J. , Sorenson Eric J. , Oskarsson Bjorn E. , Kasarskis Edward J. , Parrott Steve , Lomen-Hoerth Catherine , Murphy Jennifer , Rollins Yvonne D. , Mozaffar Tahseen , Fernandes J. Americo M. , Swenson Andrea J. , Nations Sharon P. , Shefner Jeremy M. , Andrews Jinsy A. , Koczon-Jaremko Agnes , Nagy Peter L. , Factor-Litvak Pam , Santella Rejina , Andrews Howard , Goetz Raymond , Gennings Chris , Murphy Jennifer , Floeter Mary Kay , Barohn Richard J. , Nations Sharon , Shoesmith Christen , Kasarskis Edward , Harms Matthew B. , Appel Stanley , Baloh Robert , Bedlack Richard , Chandran Siddharthan , Foster Laura , Goutman Stephen , Greene Ericka , Karam Chafic , Lacomis David , Manousakis George , Miller Timothy , Pals Suvankar , Sareen Dhruv , Sherman Alex , Simmons Zachary , Wang Leo , Manousakis George , Goldstein David B. , Harms Matthew B. ,   The New York Genome Center ALS Sequencing Consortium,   Scottish Genomes Partnership,   ALS COSMOS Study Group,   PLS COSMOS Study Group,   GTAC Investigators
Published: July 2024

Abstract
Background
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting over 300,000 people worldwide. It is characterized by the progressive decline of the nervous system that leads to the weakening of muscles which impacts physical function. Approximately, 15% of individuals diagnosed with ALS have a known genetic variant that contributes to their disease. As therapies that slow or prevent symptoms continue to develop, such as antisense oligonucleotides, it is important to discover novel genes that could be targets for treatment. Additionally, as cohorts continue to grow, performing analyses in ALS subtypes, such as primary lateral sclerosis (PLS), becomes possible due to an increase in power. These analyses could highlight novel pathways in disease manifestation.

Methods
Building on our previous discoveries using rare variant association analyses, we conducted rare variant burden testing on a substantially larger multi-ethnic cohort of 6,970 ALS patients, 166 PLS patients, and 22,524 controls. We used intolerant domain percentiles based on sub-region Residual Variation Intolerance Score (subRVIS) that have been described previously in conjunction with gene based collapsing approaches to conduct burden testing to identify genes that associate with ALS and PLS.

Results
A gene based collapsing model showed significant associations with SOD1, TARDBP, and TBK1 (OR = 19.18, p = 3.67 × 10–39; OR = 4.73, p = 2 × 10–10; OR = 2.3, p = 7.49 × 10–9, respectively). These genes have been previously associated with ALS. Additionally, a significant novel control enriched gene, ALKBH3 (p = 4.88 × 10–7), was protective for ALS in this model. An intolerant domain-based collapsing model showed a significant improvement in identifying regions in TARDBP that associated with ALS (OR = 10.08, p = 3.62 × 10–16). Our PLS protein truncating variant collapsing analysis demonstrated significant case enrichment in ANTXR2 (p = 8.38 × 10–6).

Conclusions
In a large multi-ethnic cohort of 6,970 ALS patients, collapsing analyses validated known ALS genes and identified a novel potentially protective gene, ALKBH3. A first-ever analysis in 166 patients with PLS found a candidate association with loss-of-function mutations in ANTXR2.