Back

TRIBES: A user-friendly pipeline for relatedness detection and disease gene discovery

Twine, N. A.; Szul, P.; Henden, L.; McCann, E. P.; Blair, I. P.; Williams, K. L.; Bauer, D. C.

2019-07-02 bioinformatics
10.1101/686253 bioRxiv
Show abstract

SummaryTRIBES is a user-friendly pipeline for relatedness detection in genomic data. TRIBES is the first tool which is both accurate up to 7th degree relatives (e.g. third cousins) and combines essential data processing steps into a single user-friendly pipeline. Furthermore, using a proof-of-principle cohort comprising amyotrophic lateral sclerosis cases with known relationship structures and a known causal mutation in SOD1, we demonstrated that TRIBES can successfully uncover disease susceptibility loci. TRIBES has multiple applications in addition to disease gene mapping, including sample quality control in genome wide association studies and avoiding consanguineous unions in family planning.\n\nAvailabilityTRIBES is freely available on GitHub: https://github.com/aehrc/TRIBES/\n\nContactnatalie.twine@csiro.au\n\nSupplementary informationXXXX

Matching journals

The top 1 journal accounts for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 0.1%
55.6%
Similar papers in this journal
50% of probability mass above
2
G3 Genes|Genomes|Genetics
◐ 351 papers in training set
Top 0.9%
5.5%
Similar papers in this journal
3
Bioinformatics Advances
◐ 203 papers in training set
Top 0.9%
5.5%
Similar papers in this journal
4
Frontiers in Genetics
○ 230 papers in training set
Top 1%
2.8%
Similar papers in this journal
5
Genome Research
● 468 papers in training set
Top 3%
2.4%
Similar papers in this journal
6
GENETICS
◐ 483 papers in training set
Top 2%
2.1%
7
Genetic Epidemiology
○ 55 papers in training set
Top 0.3%
2.1%
8
G3: Genes, Genomes, Genetics
◐ 252 papers in training set
Top 3%
1.7%
9
BMC Bioinformatics
○ 457 papers in training set
Top 4%
1.5%
10
Journal of Open Source Software
● 25 papers in training set
Top 0.3%
1.3%
11
BMC Genomics
○ 406 papers in training set
Top 6%
1.1%
12
European Journal of Human Genetics
○ 58 papers in training set
Top 0.8%
1.1%
13
Scientific Reports
○ 3612 papers in training set
Top 67%
1.0%
14
Briefings in Bioinformatics
◐ 354 papers in training set
Top 6%
1.0%
15
Genes
○ 144 papers in training set
Top 3%
1.0%
16
Disease Models & Mechanisms
139 papers in training set
Top 2%
0.9%
17
Nucleic Acids Research
◐ 1281 papers in training set
Top 13%
0.9%
18
PeerJ
◐ 308 papers in training set
Top 11%
0.8%
19
PLOS Computational Biology
● 1863 papers in training set
Top 20%
0.8%
20
Methods in Ecology and Evolution
○ 176 papers in training set
Top 2%
0.8%
21
Human Mutation
○ 34 papers in training set
Top 0.6%
0.6%
22
Molecular Biology and Evolution
◐ 542 papers in training set
Top 5%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.