Genomics Publication Classification
Training Document
A. Intended Goal
We are conducting this analysis to better understand the latest trends in genomics research.
The portal will guide you through multiple publication abstracts. You will be required to select
the most relevant application category for each publication
B. Registration Process
Step 1
Register and create an account on : ​https://crowdlabel.indico.io/register
Step 2
Fill out the following form: ​https://goo.gl/i39fHC
Make sure to submit your registered Indico crowdlabel email id from Step 1
Step 3
- You will receive a confirmation email
- Go to ​https://crowdlabel.indico.io/login?next=%2Fmanage​ to access your datasets
- Click on “Label” to launch the labeling portal
C. Layout Description
1. The ​left panel​ will display the t​ itle​, ​abstract​ and​ link​ for one publication at a time.
2. Use the ​right panel​ to select the application category.
3. Press ​next ​or the enter key to move onto the next publication
D. Classification Instructions
1. Read the Title and the Abstract of the article
2. Understand the general theme and the intended application of the article
3. Select only ​one ​application category on from the options. Please select the most
relevant application
4. Only ​Reject​ when there are incomplete titles or abstracts displayed in the window.
E. Application Descriptions
Application
Definition
Gene Expression
•​Analysis of RNA transcripts
SNP Genotyping
•​Analysis of single nucleotide polymorphisms (SNPs) and their association with health and
disease states
CNV Analysis
•​Analysis of copy number variations (CNVs), a form of structure variation where sections of
DNA are repeated in large numbers
DNA Sequencing
•​Determination of the sequential base pairs in the genome
miRNA Analysis
•​Analysis of miRNA and other non-coding RNA, which function as regulators of gene
expression
(including all ncRNA)
Rare Mutation
Analysis
•​Analysis of mutations found in less than 5% of cells / DNA in a sample (as low as 0.01%)
Cell-Free DNA
•​Analysis of DNA circulating freely in the (often maternal) bloodstream
Seq. detection
•​Detection of specific nucleic acids in a sample (e.g., absence / presence of DNA from a
viral particle, mouse genotyping)
(Absence /
Presence)
Absolute
Quantitation
•​Digital quantitation of the absolute (rather than relative) number of DNA particles present
in a sample, without relying on predetermined standards; often used for NGS library
preparation
Methylation
Analysis
•​Analysis of a specific epigenetic modification that adds a methyl group to DNA motifs
(often CpG islands)
Circulating Tumor
Cells
•​Analysis of circulating tumor cells (CTCs), which are cells that have shed into the
vasculature from a primary tumor and circulate in the blood stream
Methodology
•​Development of a novel application or technology
(tech. development)
NGS sample
preparation
•​Use of a technology as a sample preparation method for NGS