science

Project MinE

Project MinE is a science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Project MinE rather than just read about it. In short: Project MinE is an independent large scale whole genome research project that was initiated by 2 patients with amyotrophic lateral sclerosis and started on World ALS Day, June 21, 2013. The symptoms of amyotrophic lateral sclerosis are caused by degeneration of motor nerve cells (motor neurons) in the spinal cord, brainstem, and motor cortex.

Key takeaways

Project MinE belongs to science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Project MinE to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Project MinE from memory before moving on to harder problems.

Reference excerpt

Project MinE is an independent large scale whole genome research project that was initiated by 2 patients with amyotrophic lateral sclerosis and started on World ALS Day, June 21, 2013. The symptoms of amyotrophic lateral sclerosis are caused by degeneration of motor nerve cells (motor neurons) in the spinal cord, brainstem, and motor cortex. The exact cause of this degeneration is unknown but it is thought that environmental exposures and genetic factors play a role in susceptibility to the disease. In 5-10% of patients the family history is positive for ALS. However, it is not always possible to establish the mode of inheritance in each pedigree and not all familial cases may suffer from a genuine Mendelian or monogenic disorder. Autosomal-dominant mutations in the C9orf72 and the SOD1 gene are found in a substantial number of familial ALS cases. Mutations in other genes (such as VAPB [2], ANG, TARDBP and FUS) have been reported, but are found at a much lower frequency and with variable penetrance, suggesting the involvement of other genes. Project MinE is a research project to systematically interrogate the human genome for both common and rare genetic variation in ALS (genetic "data mining" explains the project name). The project consists of two phases and combines a genome-wide association study (GWAS) study with whole genome sequencing:

Phase 1 of Project MinE consists of whole genome sequencing of 300 DNA samples of ALS patients to detect relevant haplotypes with high fidelity (variant calling & haplotype detection). Subsequently, expansion of the current GWAS for ALS will take place by increasing the amount of DNA samples to be investigated to 15,000 ALS samples and 20,000 healthy controls (so 35,000 samples in total) and imputation using the whole genome sequencing results will be performed. Combining these two processes will result that a relatively small group of whole genome sequenced DNA samples will extend the > 500,000 single nucleotide polymorphism (SNP) markers of a GWAS to 8,000,000 SNP markers and per definition will include ALS-relevant variation. Phase 2 of the project aims to increase the number of whole genome sequenced samples to 22,500, which includes 15,000 ALS samples and 7,500 healthy controls. High-throughput next-generation sequencing will be applied. This sample size will be large enough to reliably analyze whole genome sequencing data outside of a family context. The long-term benefit of the approach taken for project MinE is the priceless catalogue of many non-ALS whole genomes that can be used to investigate other human diseases, including Diabetes Mellitus, some types of cancer, and other neurological disorders. Project MinE is worldwide the largest genetic study for Amyotrophic Lateral Sclerosis. The work has started in the second quarter of 2013 and is a unique international collaboration between scientists, industry, social foundations and patients. On July 25, 2016, the first results were published in 2 publications in Nature Genetics leading to the discovery of NEK1 and C21orf2 as new ALS risk genes.

References

External links Official website http://www.genome.gov/GWAStudies

Worked examples

Example 1 — a first encounter with Project MinE

Start with the simplest possible case. Write down what Project MinE claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Project MinE before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Project MinE ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Project MinE

In research: Project MinE appears in science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Project MinE in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Project MinE is common in secondary-school and first-year university syllabi. It links to neighbouring topics Genome projects, so understanding it makes those chapters shorter.
In everyday life: Look for Project MinE outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Project MinE in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Project MinE means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Project MinE out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Project MinE in simple terms?

Why does Project MinE matter?

Because it connects several science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Project MinE?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Project MinE.