Hack Your Genome Workshop -part 4: Work with OpenCravat
Channel: just-dna-seq
Date: 2022-06-17

Sections dedicated to clinical cases and work with own genome of the "Hack Your Genome Workshop" – a free virtual event dedicated to providing guidance in personal genomic data analyzing, and longevity genetics.

Speaker: Olga Borysova – biologist, geneticist, mitochondria expert, and founder of MitoSpace; responsible for the reports and bio stuff

Contents:
0:00:00 - Hello-world example on OpenCravat
0:01:07     – Login at server
0:01:41     – Intro to pharmacogenetics
0:04:24     – Familiarization with OpenCravat
0:07:29     – Filters in OpenCravat
0:12:57     – Understanding of output
0:21:11     – Understanding of variant using PharmGKB.org (Pharmacogenomics Knowledge Base)
0:24:53     – Categories of Annotations in OpenCravat
0:25:26     – Annotators often used in personal genomics
0:28:19 - Clinical cases analysis
0:28:36     – Clinical case #1 - progressive muscular dystrophy
0:42:17     – when we have too many variants to analyze fast
0:44:58     – Clinical case #2 - short stature with skeletal dysplasia
0:53:10     – Using a tool CADD Exome for scoring of the deleteriousness of SNPs
1:01:19 - Work with own genome
1:01:58     – Methylation - need of supplementation
1:12:29     – Neurotransmitters
1:19:25     – Leadership genes
1:22:52     – CHRNA3 - smoking addiction
1:25:18     – DLAT - energy production

Slides: https://docs.google.com/presentation/d/1UAnBGjVf446uoWK0yb-hGE9RlbcKUPkf1s1iAQf80v0/

Folder with workshop documents: https://drive.google.com/drive/folders/1xVD4-aVnDP5DBq-Mc2WmPe3Z_L6sZ0N1 that contains:
- slides
- instruction for starting working with OpenCravat and uploading your own genome
- filters (pathogenic.json and pharm.json) that were used during the workshop


— Links from the presentation —
OpenCravat server: https://run.opencravat.org

Information about genes at GeneCards:
https://www.genecards.org/cgi-bin/carddisp.pl?gene=APOE

Information about genes at PharmGKB (Pharmacogenomics Knowledge Base):
https://www.pharmgkb.org/variant/PA166156544/prescribingInfo

Prepared filter (pathogenic.json):
https://drive.google.com/drive/folders/1xVD4-aVnDP5DBq-Mc2WmPe3Z_L6sZ0N1

ClinVar – Genomic variation as it relates to human health:
https://www.ncbi.nlm.nih.gov/clinvar/variation/3238/?new_evidence=true

OMIM – Online Mendelian Inheritance in Man:
https://omim.org/entry/619595

"The 'Warrior' COMT Val/Met Genotype Occurs in Greater Frequencies in Mixed Martial Arts Fighters Relative to Controls" (2020)
https://pubmed.ncbi.nlm.nih.gov/32132825/

"Genetics, leadership position, and well-being: An investigation with a large-scale GWAS" (2022)
https://www.pnas.org/doi/10.1073/pnas.2114271119#t02

SelfDecode – information about SNP:
https://selfdecode.com/app/snp/rs1051730/

"Gene variance in the nicotinic receptor cluster (CHRNA5‐CHRNA3‐CHRNB4) predicts death from cardiopulmonary disease and cancer in smokers" (2016)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5019278/