An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

Cartney, Ann Mc; Mahmoud, Medhat; Jochum, Michael D.; Agustinho, Daniel Paiva; Zorman, Barry; Khleifat, Ahmad Al; Dabbaghie, Fawaz; Kesharwani, Rupesh K.; Smolka, Moritz; Dawood, Moez; Albin, Dreycey; Aliyev, Elbay; Almabrazi, Hakeem; Arslan, Ahmed; Balaji, Advait; Behera, Sairam; Billingsley, Kimberley; Cameron, Daniel; Daw, Joyjit; Dawson, Eric T.; Coster, Wouter De; Du, Haowei; Dunn, Christopher; Esteban, Rocio; Jolly, Angad; Kalra, Divya; Liao, Chunxiao; Liu, Yunxi; Lu, Tsung-Yu; Havrilla, James M; Khayat, Michael M.; Marin, Maximillian G.; Monlong, Jean; Price, Stephen; Gener, Alejandro Rafael; Ren, Jimin; Sagayaradj, Sagayamary; Sapoval, Nicolae; Sinner, Claude; Soto, Daniela C.; Söylev, Arda; Subramaniyan, Arun; Syed, Najeeb; Tadimeti, Neha; Tater, Pamella; Vats, Pankaj; Vaughn, Justin N.; Walker, Kimberly; Wang, Gaojianyong; Zeng, Qiandong; Zhang, Shangzhe; Zhao, Tingting; Kille, Bryce; Biederstedt, Evan; Chaisson, Mark; English, Adam C.; Kronenberg, Zev; Treangen, Todd J.; Hefferon, Timothy; Chin, Chen-Shan; Busby, Ben; Sedlazeck, Fritz J.

doi:10.12688/f1000research.51477.1

Cited by 3 publications

(3 citation statements)

References 84 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…GeneVar2 145 is an update of GeneVar, 11 to help inform clinical interpretation of structural variants ( Figure 4 ). It has expanded options allowing users to upload a VCF file, while maintaining its search functionality—based on gene name-on its web interface.…”

Section: Methodsmentioning

confidence: 99%

“… 8 , 9 However, implementing a k -mer based approach to create a pool of reference k -mers of known SVs, the annotation speed of variation in new genomes might be increased. 10 , 11 k -mers have also been used in alignment-free methods, bypassing the need for reference genomes. 12 …”

Section: Introductionmentioning

confidence: 99%

“…Together the projects of this hackathon represent a range of fields, a range of academic, industry, and government researchers, and a range of desired impacts in the field of SV analysis. Topical introductions to the specific work of each group can be found below, except from “nibSV” which was reported previously 11 and did not achieve significant progress.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

et al. 2022

Self Cite

View full text Add to dashboard Cite

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis

et al. 2022

Self Cite

View full text Add to dashboard Cite

There is a strong genetic contribution to Amyotrophic lateral sclerosis (ALS) risk, with heritability estimates of up to 60%. Both Mendelian and small effect variants have been identified, but in common with other conditions, such variants only explain a little of the heritability. Genomic structural variation might account for some of this otherwise unexplained heritability. We therefore investigated association between structural variation in a set of 25 ALS genes, and ALS risk and phenotype. As expected, the repeat expansion in the C9orf72 gene was identified as associated with ALS. Two other ALS-associated structural variants were identified: inversion in the VCP gene and insertion in the ERBB4 gene. All three variants were associated both with increased risk of ALS and specific phenotypic patterns of disease expression. More than 70% of people with respiratory onset ALS harboured ERBB4 insertion compared with 25% of the general population, suggesting respiratory onset ALS may be a distinct genetic subtype.

show abstract

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Leonard

Murtadha²,

Martínez-Carrasco³

et al. 2023

npj Parkinsons Dis.

View full text Add to dashboard Cite

Open science and collaboration are necessary to facilitate the advancement of Parkinson’s disease (PD) research. Hackathons are collaborative events that bring together people with different skill sets and backgrounds to generate resources and creative solutions to problems. These events can be used as training and networking opportunities, thus we coordinated a virtual 3-day hackathon event, during which 49 early-career scientists from 12 countries built tools and pipelines with a focus on PD. Resources were created with the goal of helping scientists accelerate their own research by having access to the necessary code and tools. Each team was allocated one of nine different projects, each with a different goal. These included developing post-genome-wide association studies (GWAS) analysis pipelines, downstream analysis of genetic variation pipelines, and various visualization tools. Hackathons are a valuable approach to inspire creative thinking, supplement training in data science, and foster collaborative scientific relationships, which are foundational practices for early-career researchers. The resources generated can be used to accelerate research on the genetics of PD.

show abstract

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

Cited by 3 publications

References 84 publications

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Contact Info

Product

Resources

About