Resources for Scientists
The following is an adaptation of ALS relevant resources compiled by Lyle Ostrow, MD, PhD (Temple University) for the Department of Defense ALS web portal:
Click on the topic below to see a detailed listing ofavailable resources:
ALS Reproducible Antibody Platform (ALS RAP) – created as a public-private partnership by the ALS Association, the Motor Neurone Disease Association (UK), and the ALS Society of Canada to ensure the availability of the highest quality, validated antibodies developed using standard operating procedures that will be openly shared with the ALS research community. Notably, no form of intellectual property protection or patents will be filed for all new reproducible antibodies fully discovered and developed by ALS-RAP. This collaborative effort, based on open science and complete freedom to operate, will ensure the use of the highest-quality tools to increase the success of future drug discovery.
Target ALS Antibody Core – Currently available:
- Poly(GP)monoclonal antibodies from two hybridoma clones. Both have been deposited at the Developmental Studies Hybridoma Bank (DHSB).
- Mouse Vacht polyclonal antibody. Investigators can request up to 10 aliquots (20 ul/aliquot).
ALZForum ALS Mouse Model Database – Organized phenotypic information to facilitate comparisons between over 40 ALS mouse models.
European Mutant Mouse Archive (EMMA) – 8,000 mutant mouse lines cryopreserved as frozen sperm and/or embryos. Includes several ALS-relevant strains with mutations in FUS, Tardbp, OPTN, and others.
Jackson Labs ALS Mouse Model Resource – The Jackson Laboratory’s website to identify and select ALS mouse models and to find multiple helpful resources.
Mutant Mouse Resource & Research Center – NIH-funded mouse lines and embryonic stem (ES) cells, as well as related products and services.
Bloomington Drosophila Stock Center (BDSC) ALS Fly Models – Collects, maintains, and distributes Drosophila melanogaster strains for research. Includes strains with mutations in SOD1, Alsin, SETX, FUS, VAPB, ANG, TARDP, FIG4, OPTN, ATXN2, UBQLN2, PFN1, TAF15, and EWSR1. Also has multiple C9orf72-relevant mutant strains with different GGGCC expansions.
The Zebrafish Information Network (ZFIN) – A database resource for the laboratory use of zebrafish genetic models. Part of the Alliance of Genome Resources. Information on multiple ALS Zebrafish models, including SOD1 and TARDBP mutants.
Alliance of Genome Resources – A consortium of 6 model organism databases and the Gene Ontology (GO) Consortium whose goal is to provide an integrated view of their data in order to facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, heath, and disease. The Alliance includes FlyBase, The Mouse Genome Database, The Gene Ontology Consortium, The Saccharomyces Genome Database, The Rat Genome Database, WormBase, and The Zebrafish Information Network.
NEALS Sample Repository
NEALS has a repository of serum, plasma, cerebrospinal fluid (CSF), whole blood, extracted DNA, and urine samples from NEALS and NCRI research studies of amyotrophic lateral sclerosis (ALS) and motor neuron disease. Repository support has included funding from The ALS Association and Project ALS. Samples from this repository are available to researchers for the purpose of furthering the understanding of ALS or motor neuron disease and developing disease biomarkers.
Target ALS Postmortem Tissue Core
Autopsies are performed at six geographically distributed academic ALS centers (Johns Hopkins University, Barrow Neurological Institute, Columbia University, Georgetown University, University of California San Diego and Washington University St. Louis) according to strict SOPs for tissue acquisition, dissection, processing, storage, neuropathological characterization, and QC analysis – all specifically optimized for ALS research. A web-based searchable database of the postmortem tissue inventory provides estimates of fixed and frozen tissues available that meet basic demographic criteria. More detailed case characteristics request and tissue regions can be requested using the Target ALS PM Core Request Form, which includes the instructions and timeline for requesting samples. Whole Genome Sequencing (WGS) and bulk tissue RNA-Seq for multiple central nervous system (CNS) regions are performed centrally at the New York Genome Center (NYGC) on all autopsies, and raw data files in multiple formats are made immediately available (via Genetic Data Request Form). The de-identified genomic, transcriptomic, and phenotypic data can also be visualized and explored using the MetroNome Visual Data Exploration Platform. This is the most comprehensive, modern ALS specific autopsy bank in the USA.
Department of Veteran Affairs Biorepository Brain Bank (VABBB)
Collects, processes, stores, and gives out neurological tissue specimens from Veterans who died from ALS or related motor neuron disorders (PLS, PMA, PBP). Veterans without ALS or other neurological diseases (Non-Neurological Controls) are also collected. Downloadable description of tissue inventory and separate brochure for investigators. Tissue Request Forms may be requested from Dr. Ian Robey via email (Ian.Robey@va.gov).
Netherlands Brain Bank (NBB)
Part of the BrainNet Europe II, the NBB contains >4,000 autopsies with a variety of neurological and psychiatric disorders, and non-demented controls. Also provides CSF, plasma, and sometimes spinal cord and dorsal root ganglia. There is online access to search the NBB database (requires registering for an account), and detailed information on the sample request and review process, including downloadable application forms.
Postmortem Brain Tissues collected at six academic centers (University of Miami, University of Maryland, Harvard, the Human Brain and Spinal Fluid Resource Center, Mt. Sinai Brain Bank, University of Pittsburgh). Not specific for ALS, but contains ALS autopsies. Has an online inventory search website and detailed online instructions for obtaining tissues.
UK Brain Banks Network
MRC directed national network of UK Brain Banks using common protocols to collect and store tissues. The network provides high quality brain tissue to academic and industry researchers in the UK and internationally. Not ALS specific, but includes motor neuron disease autopsies at many centers. Researchers can use an online searchable database (requires registration), which contains details of the samples available.
Answer ALS iPS Cells & Motor Neurons – The Answer ALS Research Project entails creating up to 1,000 unique stem cell (iPSC) lines from ALS patient participants and healthy controls. Cedars-Sinai is leading the generation of the iPSCs and their derived motor neurons from patient blood samples collected across the multiple AnswerALS sites. For information on ordering iPSCs Lines, click here. Linked clinical, genetic, molecular, and biochemical data can be explored in the Answer ALS Data Portal, and used to select and order the corresponding cell lines.
CDC National ALS Registry Biorepository – Multiple types of biosamples collected from persons with ALS who are enrolled in the National ALS Registry. For information on requesting data and/or samples, click here.
Cedars Sinai Induced Pluripotent Stem Cell Core – The Core is involved in many ALS projects, including Answer ALS and NeuroLINCS. They have a searchable online database of ALS cell lines, including ALS, PLS, non-ALS MND, and SMA lines.
CReATe Consortium Biorepository – Funded by the Rare Diseases Clinical Research Network (RDCRN) of NIH. Samples are collected by multiple Consortium sites from patients participating in the Phenotype-Genotype-Biomarker (PGB) protocol (NCT02327845). For biofluid collection SOPs, click here. Includes longitudinal samples from patients with ALS, ALS-FTD, PLS, PMA, HSP, and MSP.
NEALS Sample Repository – Biofluid samples collected from numerous ALS clinical trials and biofluid collection efforts of the Northeast ALS Consortium. To apply for samples, please visit the NEALS Sample Request Portal.
NeuroLINCS – NIH funded collaborative effort between research groups with expertise in iPSC technology, disease modeling, OMICS, and computational biology. The data pagehas links to multiple ALS and SMA iPSC-derived data sets as either raw (accessed via dbGaP or Chorus) or processed (accessed via LINCS Data Portal) transcriptomic, proteomic, epigenomic data collected by participating sites.
- The DNA Bank: >3,000 blood samples, stored at CIGMR (Centre for Integrated Genomic Medical Research) in Manchester, UK; also has clinical information (divided into a minimum and extended dataset) available to researchers.
- The Cell Lines Collection: A sub set of the DNA Bank samples as lymphoblastoid cell lines and peripheral blood lymphocytes; enable the creation of induced Pluripotent Stem Cells (iPSCs).
- The Epidemiology Collection: >200 patient and matched control surveys including extensive environmental and lifestyle data (both from self-report questionnaires and telephone interviews) as well as a subset of genomic DNA samples.
CDC National ALS Biorepository – Postmortem tissues include brain, spinal cord, bone, and muscle from 50 ALS patients who were enrolled in the CDC National ALS Registry. To request samples and data, visit the national ALS Biorepository Researcher Information page.
Department of Veteran Affairs Biorepository Brain Bank (VABBB) – Neurological tissue specimens from Veterans who died from ALS, and more recently has added enrollment of non-ALS Registry veterans. Phenotype data includes semi-annual ALSFRS-R/EX, with additional postmortem proxy interview, cognitive assessments, detailed health information from surveys and VA electronic medical records. Investigators are encouraged to discuss their requests with the VABBB before applying, by contacting Dr. Ian Robey at 520-792-1450 x4436 or Ian.Robey@va.gov.
Johns Hopkins ALS Postmortem Core (collaboration with the CDC National ALS Registry). Frozen and fixed CNS tissues, liver, and muscle samples from 120+ ALS/MND and non-neurological control autopsies, linked to de-identified clinical, demographic, neuropathological, genomic, and QC data. Whole Genome Sequencing (WGS) and bulk tissue RNA-Seq for multiple central nervous system (CNS) regions are also available from the NYGC ALS Consortium – linked to the tissue samples and slides. Email Dr. Lyle Ostrow – Lostrow1@jhmi.edu for more information and a sample request form.
Netherlands Brain Bank (NBB) – The NBB contains >4,000 autopsies with a variety of neurological and psychiatric disorders, and non-demented controls. Also banks CSF, plasma, and sometimes spinal cord and dorsal root ganglia. There is online access to search the NBB database (requires registering for an account), and detailed information on the sample request and review process, including downloadable application forms.
NIH NeuroBioBank – Postmortem Brain Tissues collected by six biorepositories (University of Miami, University of Maryland, Harvard, the Human Brain and Spinal Fluid Resource Center, Mt. Sinai Brain Bank, University of Pittsburgh). Not specific for ALS, but contains ALS autopsies. Has an online inventory search website and detailed online instructions for obtaining tissues.
Target ALS Postmortem Tissue Core – Autopsies are performed at five academic ALS centers (Barrow Neurological Institute, Columbia University, Georgetown University, University of California San Diego, and Washington University St. Louis) according to harmonized SOPs for tissue dissection and clinical data collection. Whole Genome Sequencing (WGS) and bulk tissue RNA-Seq for multiple central nervous system (CNS) regions are available from the NYGC ALS Consortium. For any questions or to inquire about new or existing tissue requests, please email Marina Selenica at email@example.com.
UK Brain Banks Network – Supplies tissue samples to academic and industry researchers in the UK and internationally from multiple participating brain banks. Not ALS specific, but includes motor neuron disease autopsies at many centers.
ALS Online Database (ALSoD) – collates information about genes and genetic variants connected to ALS. Includes links to publications and summary information on each gene, strength of evidence, lists of variants, and phenotype visualizations incorporating age of onset, sex, site of onset, family history, and variant type.
Answer ALS Data Portal – Incorporates de-identified clinical information on 1,200+ participants, linked to comprehensive genomic, epigenomic, proteomic, and transcriptomic data. The data can be explored with multiple analysis and visualization tools, downloaded, and used to identify and order the corresponding Answer ALS Cell Lines.
CDC National Amyotrophic Lateral Sclerosis (ALS) Registry – Congressionally mandated program to collect, manage, and analyze data about persons with ALS. Extensive demographic and risk factor data is available, including residential and occupational histories, toxic and environmental exposures, family history, trauma, military history, and more. There is an online Research Application Form to request access to the data.
ClinGen ALS Gene-Disease Validity Classification Reports – ClinGen is an NIH-funded resource dedicated to defining the clinical relevance of genes and variants for use in precision medicine and research. The ALS Gene Curation Expert Panel, chaired by ALSRP Programmatic Panel member Dr. Matthew Harms, MD, evaluates the evidence for genes that have been linked to the phenotype of ALS, and generates detailed classification reports for each gene.
Database of Genotypes and Phenotypes (dbGaP) – Archives and distributes data and results from studies examining the interaction of genotype and phenotype in humans.
Hammell Lab (at CSHL) Bioinformatics Software for high throughput sequencing analysis, particularly useful in analysis of transposable elements and other repetitive sequences. Have been used to analyze the NYGC ALS Consortium data (see manuscript) and for several other ALS-retrotransposon projects.
NEALS Historical Trial Data – De-identified data from multiple ALS trial databases, available for researchers to mine. To request access to NEALS data please fill out the Data Request Form and submit to: Tara Lincoln, NEALS Director of Operations, at firstname.lastname@example.org.
NYGC ALS Consortium – A partnership of clinicians, basic scientists, geneticists, and computational biologists from 42 institutions around the globe to apply whole genome sequencing and functional genomics to the study of ALS. The current dataset contains WGS data from >4,300 ALS cases and >1,800 controls, linked to harmonized clinical phenotype data. For more information, contact email@example.com.
Pooled Resource Open-Access ALS Clinical Trials (PRO-ACT) Database – Over 10,700 fully de-identified clinical patient records from the placebo and treatment-arm data of 23 Phase II/III Clinical Trials. Includes demographic, lab, medical, and family history, and other data elements. More than 10 million longitudinally collected data points.
Project MinE – Project to perform whole-genome sequencing (WGS) of 15,000 ALS patients and 7,500 controls. The current dataset >10,900 DNA profiles, of which >6,000 profiles are available via an online open-access Data Browser. There is an online form to request the WGS and GWAS data sets.
NYGC ALS Spatial Transcriptomics Portal – An interactive data exploration portal for the spatial transcriptome atlas of the ALS spinal cord. Includes multiple time points in G93A and wildtype mice, and postmortem human spinal cord. Downloadable user guide and companion manuscript.
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