Frequently Asked Questions

General:

What is the ALS Knowledge Portal and how do I use it?

The ALS Knowledge Portal (ALSKP) enables browsing, searching, and analysis of human genetic information linked to amyotrophic lateral sclerosis and related traits, while protecting the integrity and confidentiality of the underlying data. The ALSKP is similar to the Project MinE Variant Browser, which is an excellent resource for displaying variants from ALS whole genomes.

How should I cite the ALS Knowledge Portal?

Please use the following citation when referring to data accessed via this portal: Amyotrophic Lateral Sclerosis Knowledge Portal. Year Month Date of access; URL of page you are citing. Also, please cite Farhan et al., 2018 BioRxiv: https://www.biorxiv.org/content/10.1101/307835v2.

Technical:

What types of data are in the ALS Knowledge Portal?

Exome data from 3,864 ALS cases and 7,839 ethnically matched non-ALS controls. We also display frequencies for each variant from gnomAD.

What is the ethnicity of samples?

All samples were reported as Caucasian and this was confirmed by PCA.

Which genome assembly does ALS Knowledge Portal use as a reference?

GRCh37/hg19

If you used exome sequencing, why are there intronic variants?

In addition to exons, regions from adjacent introns may be covered in whole exome sequencing. These regions have been included in the ALSKP because they may impact protein expression (e.g., splice sites).

How do I report a data error or bug in the database?

We welcome your feedback! Please contact us at help@alskp.org.

I have more questions that are not listed here, who should I contact?

Please contact Sali Farhan: sfarhan@broadinstitute.org.

Additional resources:

Hail
Project MinE
ALS Variant Server
HEX
gnomAD
GTEx
ClinVar
Neale Lab
Stanley Center
Program in Medical and Population Genetics
Center for Genomic Medicine