Hack Your Genome Workshop
Channel: just-dna-seq
Date: 2022-06-10

A free virtual event dedicated to providing guidance in personal genomic data analyzing, and longevity genetics.

The workshop explains:

*   how to analyze your personal genome with an open-source platform
*   how to choose modules for investigating different aspects of your genome (health risk prediction, personal drug response, etc.)
*   which longevity genes databases exist and how genetics affects our lifespan

Contents:
0:00:00 - Introduction
0:01:41 - Personal genomics (Anton Kulaga)
0:02:10    ● step 1. Sequence yourself
0:02:13      ○ Existing personal genetics
0:04:43    ● step 2. Bioinformatic pipeline (Newton Winter)
0:04:49      ○ Genomic pipelines
0:06:30      ○ Human Genome Sequencing
0:08:21      ○ Deep-learning on genomic variants
0:09:26      ○ Types of mutations
0:11:30      ○ How deep-variant caller works
0:13:12    ● step 3. Annotation of VCFs (Anton Kulaga)
0:13:42      ○ problem 1. Choosing of annotators
0:14:38    ● step 4. Analysis of annotations
0:14:42      ○ problem 2. Choosing of fields in annotations
0:15:11      ○ GitCoin
0:18:18 - Longevity Genetics
0:18:59    ● Heritability of diseases and traits
0:21:42    ● Genetics of longevity
0:22:42      ○ Numbers of centenarians
0:24:17      ○ Determinants of exceptional human longevity
0:26:17      ○ high level of HTT intermediate alleles in centenarians
0:27:53      ○ Databases on aging
0:30:44    ● Example of longevity genes (Olga Borysova)
0:34:13      ○ UCP genes
0:36:04      ○ Introduction to mitochondria metabolism for not biologists
0:39:11      ○ Uncoupling mechanism in mitochondria - UCP protein
0:41:02      ○ Brown fat - fat for fat burning
0:42:21      ○ Association of uncoupling with longevity
0:43:38      ○ When your brain boils - releasing of neurotransmitter - USP2 protein
0:44:44      ○ Uncouplers as potential drugs for age-related diseases
0:46:57 - Intro to OpenCravat/OakVar (Ryangguk Kim)
0:48:46    ● History of OpenCravat/OakVar
0:50:49    ● Principle of work of OakVar
0:57:30    ● Availability to sequencing and genomic analysis
0:59:39    ● Analysis using Python Jypyter Notebook
1:00:04    ● Analysis using R Studio
1:00:26    ● Analysis in web browser
1:00:38    ● Custom web app
1:01:27    ● Getaway to AI on genomics
1:02:57 - Hello-world example on OpenCravat (Olga Borysova)
1:04:04    ● Login at server
1:04:38    ● Intro to pharmacogenetics
1:07:20    ● Familiarization with OpenCravat
1:10:26    ● Filters in OpenCravat
1:15:53    ● Understanding of output
1:24:05    ● Understanding of variant using PharmGKB.org (Pharmacogenomics Knowledge Base)
1:27:50    ● Categories of Annotations in OpenCravat
1:28:23    ● Annotators often used in personal genomics
1:31:14 - Clinical cases analysis
1:31:32    ● Clinical case #1 - progressive muscular dystrophy
1:45:10    ● when we have too many variants to analyze fast
1:47:55    ● Clinical case #2 - short stature with skeletal dysplasia
1:56:06    ● Using a tool CADD Exome for scoring of the deleteriousness of SNPs
2:04:15 - Work with own genome
2:04:53    ● Methylation - need of supplementation
2:15:26    ● Neurotransmitters
2:22:22    ● Leadership genes
2:25:44    ● CHRNA3 - smoking addiction
2:28:15    ● DLAT - energy production
2:32:21 - Polygenic risk scores (Alina Fedorova)
2:34:18    ● What kind of data to we have to work with?
2:37:29    ● Why ML approach
2:38:13    ● What is polygenic risk score (PRS)?
2:38:54    ● Calculating dosage
2:39:33    ● A linear regression framework with regularization
2:41:00    ● Prediction of observations through PRS construction
2:41:39    ● Comparison of predictive performance of different methods
2:42:29    ● Choosing a polygenic risk score
2:44:04    ● Information needed from the original PRS
2:45:14  - Using public PRS (Alex Karmazin)
2:46:49    ● Implementation PRS in OpenCravat
2:50:28    ● Using PRS with OpenCravat
2:50:50      ○ Percentile identification
2:52:57      ○ Population identification
2:56:53 - Extras (Anton Kulaga)
2:59:20    ● Future plans
3:06:25    ● Recommendations for communities to join
3:09:34 - Q&A
3:29:24 - OPTIONAL gene editing and “bioweapons” module
3:30:48    ● What if I am unhappy with my genetic variations?
3:31:55    ● A tool for genome editing: CRISPR-Cas9
3:34:00    ● Comparison of gene-editing technologies
3:36:41    ● Actions and mistakes of Dr. He Jiankui
3:39:54    ● About CCR5 gene
3:41:23    ● Super human genes
3:44:07    ● Using Synthego.com
3:47:55    ● Design DNA vector with VectorBuilder.com
3:58:21    ● Self (not)use recommendations
4:04:03 - Q&A (2)
4:04:35    ● Delivery
4:08:46    ● Useful cases

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