Answer ALS

Data Portal

We are building the most comprehensive clinical, genetic, molecular & biochemical assessment of ALS, while openly sharing the results with the global research community. The Answer ALS data portal is designed to help scientists mine this wealth of data and resources, accelerate their research and ultimately, advance the development of effective therapeutics for ALS.

Data Portal 2.0 Coming Soon

Answer ALS | Preview of data portal

2.6T number of data points released to date – by program’s end this will be 20 trillion!

1000+ participant clinical, genomic, transcription, and protein expression data types collected

100% data generated by Answer ALS is being made available to the global research community

Metadata & Clinical data

Answer ALS has collected clinical data on 1000+ enrolled participants. All data is available to download and has been deidentified according to HIPAA standards. You can download the metadata at any time without a DUA but will need approval to download the corresponding assay data.

We’ve completed patient enrollment and are now actively working through the data generation phase. Stay tuned for Release 3.0 in the next coming months.

Summary Charts

To learn more about the disease, we enrolled over 1,000 patients. Here is a small sampling of the data we collected. Download our latest release for yourself to explore further.

Answer ALS Experiments Overview

Answer ALS is an ongoing research program building a comprehensive collection of datasets characterizing the biology of 1000 ALS patients.

The Answer experimental design helps to address possible variabilities commonly found in larger OMICs experiments. There are four steps that can introduce variation; sample and data collection, sample shipping , sample processing and data standardization.

For sample collection, all samples collected at clinical sites were sent to Cedars Sinai for processing and also to NYGC for whole genome sequencing. Induced pluripotent stem cell lines and motor neurons were generated in the same lab with consistent personnel. Batch and technical controls were included to help identify any possible variation generated during production. Below are descriptions of the lines produced.

  • iPSCs Lines: Derived induced pluripotent stem cells (iPS cells or iPSCs) from participant blood donations to the Answer ALS study. These lines are available through Cedars Sinai Biomanufacturing Center. To learn more, visit the Cedars Sinai Biomanufacturing Center Website.
  • Motor Neurons: The iPSCs are differentiated into spinal motor neurons according to the direct iPSC-derived motor neuron (diMNs) protocol developed by Cedars Sinai. These lines are generated through the leadership of Dr. Svendsen and Dr. Sareen both at Cedars Sinai. You can download a protocol for culturing or collecting the cells through the hyperlinks.
  • Batch and Technical Control: The CTRL-NEUEU392AE8 is used as a technical and differentiation batch control.
    • Batch technical control (BTC): 2AE8iCTR-n6 line serves as BTC and was produced in bulk Oct-Dec 2018. Each OMICs lab is sent a vial from this differentiation with each shipment to run with all the other vials in the shipment. This controls for ‘Omics assay-specific variability'; since BTC pellets were produced at the same time with an SOP, a given assay should return the same results for any BTC pellet.
    • Batch differentiation control (BDC): 2AE8iCTR-n6 line is also differentiated with every group of differentiations. This controls for inter batch variability in differentiation. This line is thawed, expanded, differentiated, and pelleted in addition to the ALS/CTR lines in each batch. OMICs labs receive BDC pellets along with ALS/CTR pellets for each differentiation batch.

Assays

This data is available for download by request. Please visit the data search or download page for information on how to access.

Genomics

Answer ALS | Genomics

Each participant enrolled through the Answer ALS project has their genome sequenced by The New York Genome Center's Center for Genomics of Neurodegenerative Disease (NYGC-CGND). These datasets are generated through the leadership of Dr. Finkbeiner at the Gladstone Institutes.

Epigenomics

Answer ALS | Metabolomics

ATAC-Seq is a transposase-based, deep sequencing based epigenomic assay used to assess chromatin accessibility and identify functional regulatory sites involved in driving transcriptional changes associated with cellular response. These datasets are generated through Diagenode and MIT under the leadership of Dr. Fraenkel.

Proteomics

Answer ALS | Proteomics

We perform SWATH-MS (Sequential Window Acquisition of all THeoretical fragment ion spectra by Mass-Spectrometry), a data-independent acquisition (DIA) method. These datasets are generated under the leadership of Dr. Van Eyk at Cedars Sinai.

Transcriptomics

Answer ALS | Transcriptomics

RNA-Seq is a deep sequencing approach to transcriptome profiling. Studies using this method will precisely measure the extent and complexity of transcriptional perturbations in iPSC derived motor neurons. These datasets are generated at UCI under the leadership of Dr. Thompson.

Data Levels

Datasets are provided by this portal at multiple stages in processing, which are designated as "data levels." A definition can be found here.

Level 1
Level 2
Level 3
Level 4
Level 5
Genomics
.fastq
.cram
.raw.vcf
.vcf (joint call)
Epigenomics
.fastq
.bam
.narrowPeaks
.bed (diff. regions)
Transcriptomics
.fastq
.bam
.tsv
.tsv (diff. genes)
Proteomics
.wuff
.mzML
.tsv
.tsv (diff. proteins)

Level 1

Level 1 data is raw, immutable data coming off an instrument (e.g. a sequencer).

Level 2

Level 2 data is raw data mapped against the appropriate reference.

Level 3

Level 3 data the most processed form of patient-specific data.

Level 4

Level 4 data is attained from the joining of a cohort of patients' level 3 data from a particular assay.

Level 5

Level 5 data is attained from the integration of level 4 datasets across omics assays. Level 5 data represents the knowledge ultimately resulting from the experiment.

A special thank you to each and every one of our program participants and partners.

Please visit our main site to view the full list of our supporters.