Connecting the Dots: Biology At Scale In The Age Of AI (Broad Institute)

Collected the videos in a playlist 

Connecting the Dots: Biology At Scale In The Age Of AI (Broad Institute)

Nov 9, 2024

1,338 views • Nov 9, 2024

SESSION 1 BRIDGING THE GAP: MODELS FOR BIOLOGICAL PREDICTION Chair: Wengong Jin (MIT) Hilary Finucane (Broad) Mehrtash Babadi (Broad) Keynote II: Alex Rives (Broad) For more information visit: https://www.broadinstitute.org

Meet Evo, the DNA-trained AI that creates genomes from scratch

https://www.science.org/content/article/meet-evo-dna-trained-ai-creates-genomes-scratch ChatGPT, the famous artificial intelligence (AI) chatbot, can summarize Moby Dick, write computer code, and serve up a recipe for chicken à la king because it has much of the written information on the internet at its silicon fingertips. What if it could do the same for DNA?

That’s the advance behind a new study published today in Science. Researchers describe an AI model, schooled on billions of lines of genetic sequences, that can deduce how bacterial and viral genomes operate and use that information to design new proteins and even whole microbial genomes. The model, known as Evo, could help scientists probe evolution, investigate diseases, develop new treatments, and potentially answer a host of other biomedical questions.

“This work is extremely significant,” says computational biologist Arvind Ramanathan of Argonne National Laboratory, who wasn’t connected to the study. The tests the authors put Evo through, he says, provide “a great showcase of applications” for the AI.

HGVS nomenclature

 Was recently asked about HGVS nomenclature reporting. The fun thing about biology is that there's going to be exceptions to the rule or some shenanigans that you didn't expect when setting out a rule. 

"The Human Genome Variation Society (HGVS) provides standardized recommendations for describing human sequence variants, which are widely accepted in the scientific community, especially in the practice of clinical molecular pathology.1 Use of the HGVS nomenclature system is a de facto recommendation for clinical reporting of sequence variants.2, 3 Being a core component of the clinical report, incorrect HGVS nomenclature can have a negative impact on patient care, such as misdiagnosis or clinical trial ineligibility. HGVS nomenclature has been traditionally computed manually by pathologists from Sanger sequencing electropherograms. However, manually computing HGVS nomenclature is time consuming, complex, and error prone, particularly with insertion and deletion (indel) variants, resulting in inconsistencies across laboratories."

Source:Clinical Implementation and Validation of Automated Human Genome Variation Society (HGVS) Nomenclature System for Next-Generation Sequencing–Based Assays for Cancer

In the 25th Anniversary Special Issue of Human Mutation, Den Dunnen et al. (2016) publish an update of the Human Genome Variation Society (HGVS) recommendations for the description of sequence variants (http://www.HGVS.org/varnomen). One of the issues discussed is how widespread HGVS nomenclature is used and, when used, whether published variant descriptions correctly follow the recommendations. An EGFR (OMIM# 131550) lung cancer testing scheme assessed in January 2016 by the United Kingdom National External Quality Assessment Scheme (UK NEQAS) for Molecular Genetics demonstrates the current variability in the use and interpretation of the HGVS guidelines by diagnostic laboratories based across the globe.

Source: HGVS Nomenclature in Practice: An Example from the United Kingdom National External Quality Assessment Scheme   

 

Shall explore this tool 

hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update

https://github.com/biocommons/hgvs

Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature Methods

 Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature Methods 

 

https://www.nature.com/articles/s41592-021-01254-9

Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature Methods The rapid growth of high-throughput technologies has transformed biomedical research. With the increasing amount and complexity of data, scalability and reproducibility have become essential not ... www.nature.com

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https://github.com/GoekeLab/bioinformatics-workflows    

GitHub - GoekeLab/bioinformatics-workflows: minimal example implementations for bioinformatics workflow managers Workflow managers provide an easy and intuitive way to simplify pipeline development. Here we provide basic proof-of-concept implementations for selected workflow managers. The analysis workflow is based on a small portion of an RNA-seq pipeline, using fastqc for quality controls and salmon for ... github.com

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Orientation Bias artifect

 strand bias and orientation bias – GATK (broadinstitute.org)

"

The read orientation artifact, also known as the orientation bias artifact, arises due to a chemical change in the nucleotide during library prep that results in, for example, G base-paring with A. This kind of artifact has a clear signature (e.g. C to A SNP that occurs predominantly for the middle C in the DNA sequence CCG), and it’s singlestranded in nature. Downstream, this artifact manifests as low allele fraction SNPs whose evidence for the alt allele consists almost entirely F1R2 reads or F2R1 reads. A read pair is F1R2 (forward 1st, reverse 2nd) if the sequence of bases in Read 1 maps to the forward strand of the reference (F1), and the sequence of Read 2 to the reverse strand
of the reference (R2). F2R1 is defined similarly

 

if someone has read the dragonbioit used guide in illumina, it just mentioned orientation bias, ignore the strand bias.

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Benchmarking variants and comparing truth sets: List of useful tools and publications

Just realised that other than vcf-compare and bedtools intersect 

there's other options

 

https://github.com/RealTimeGenomics/rtg-tools

https://github.com/Illumina/hap.py

 

Also there's actually new variant callers ..

Molina-Mora, J.A., Solano-Vargas, M. Set-theory based benchmarking of three different variant callers for targeted sequencing. BMC Bioinformatics 22, 20 (2021). https://doi.org/10.1186/s12859-020-03926-3

 

Krishnan, V., Utiramerur, S., Ng, Z. et al. Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. BMC Bioinformatics 22, 85 (2021). https://doi.org/10.1186/s12859-020-03934-3

Additional file 23: File 3

. verify_variants.py

 

 

Zook, Justin M et al. “An open resource for accurately benchmarking small variant and reference calls.” Nature biotechnology vol. 37,5 (2019): 561-566. doi:10.1038/s41587-019-0074-6

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

hgvs.readthedocs.io/

• hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.

  Wang M, Callenberg KM, Dalgleish R, Fedtsov A, Fox NK, Freeman PJ, Jacobs KB, Kaleta P, McMurry AJ, Prlić A, Rajaraman V, Hart RK.Hum Mutat. 2018 Dec;39(12):1803-1813. doi: 10.1002/humu.23615. Epub 2018 Sep 5.PMID: 30129167 Free PMC article.

  • Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer.

    den Dunnen JT.Curr Protoc Hum Genet. 2016 Jul 1;90:7.13.1-7.13.19. doi: 10.1002/cphg.2.PMID: 27367167

   

• A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

  Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.Bioinformatics. 2015 Jan 15;31(2):268-70. doi: 10.1093/bioinformatics/btu630. Epub 2014 Sep 30.PMID: 25273102 Free PMC article.
• VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions.

  Freeman PJ, Hart RK, Gretton LJ, Brookes AJ, Dalgleish R.Hum Mutat. 2018 Jan;39(1):61-68. doi: 10.1002/humu.23348. Epub 2017 Oct 17.PMID: 28967166 Free PMC article.
• Clinical Implementation and Validation of Automated Human Genome Variation Society (HGVS) Nomenclature System for Next-Generation Sequencing-Based Assays for Cancer.

  Callenberg KM, Santana-Santos L, Chen L, Ernst WL, De Moura MB, Nikiforov YE, Nikiforova MN, Roy S.J Mol Diagn. 2018 Sep;20(5):628-634. doi: 10.1016/j.jmoldx.2018.05.006. Epub 2018 Jun 21.PMID: 29936258

Running Kraken2 and creating a Krona report

 Had to work with Ion Torrent BAMs for this but I think it's applicable to everything

  Needed to run this on unmapped reads so running this first.

After that the next script is fairly simple 

Will share the install when I have time. A major hiccup for me was realising not all pre-built db works with Kraken2

This command allows you to see what apps are consuming internet. ss -p

 

This command allows you to see what apps are consuming internet.

ss -p

GenomSys Banks on MPEG-G Standard to Make Genome Analysis Mobile

 This software company did something that I didn't expect... putting the variant calling on the phone itself ..

"The variant calling is run directly on the phone, extracting the data from the file on your phone, processed on the phone, and only at the end the VCF file could be shared in the cloud for annotation and reporting by an accredited physician," Ascari said. The physician is necessary to assure that the result is of "diagnostic quality," he added.

I honestly expected CRAM & cloud based calling with encrypted exchange (made feasible with 5G mobile network) of bam reads with an app store like customised reports for what you want to know about your genetics. 

Other than security concerns, I don't see why I would want variant calling on the phone though.

Previous posts

IonCRAM: a reference-based compression tool for ion torrent sequence files 

Future of Genomics: 10 bold predictions

What 5G mobile networks portends for the future of personal genomics

 

 

 

A novel BRCA2 splice variant identified in a young woman

 Sharing a newly published article where a novel c.682‐2delA variant involving the AG consensus at the 3′ end of BRCA2 intron 8 was detected. The case involved a 33‐year‐old Italian breast cancer patient belonging to a HBOC family (BRCAPro score: 88%) with no other known pathogenic BRCA mutation. 

 

A novel BRCA2 splice variant identified in a young woman - Nicolussi - - Molecular Genetics & Genomic Medicine

de novo assembly of Ion Torrent Reads

 I am intrigued that this Genome assembly guide includes mention of SOLID and Ion Torrent ... although not much information is given on how to work on them for genome assembly. 

That said, perhaps the SPADES plugin provided with the sequencer solves most of everyone's immediate needs ... Wondering how improve on evaluating the assemblies 

IonCRAM: a reference-based compression tool for ion torrent sequence files

 IonCRAM: a reference-based compression tool for ion torrent sequence files https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487613/ 

 IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. For the BAM files, IonCRAM could achieve a space saving of about 43%. This space saving is superior to what achieved with the CRAM format by about 8–9%.

Future research for reducing the space consumption of the Ion Torrent BAM files would include the binning of the flow signal and quality values. The idea of binning was initially introduced by Illumina [27] to reduce the space consumption of the quality values. This initiative was immediately followed by intensive research to optimize the binning procedure and address its effect on the downstream analysis, especially on the variant calling step [28–31]. We think that the binning of flow signals and quality data of Ion Torrent would also be successful, provided that the manufacturer contribute to this research. We added an option to IonCRAM for binning the flow signals, in a similar way to the binning method implemented in [26], and measured its effect on compression (Supplementary File 1). We left the step for investigating the effect of this binning on the downstream analysis to further research.

It is worth mentioning that IonCRAM has not been only used for the test data in the paper, it has also been used to compress and backup thousands of files for the Saudi Human Genome Program. IonCRAM is an open source and it is available for free along with the related test data at the tool website http://ioncram.saudigenomeproject.com.

  

Static ip on Jessie Raspbian with dhcpcd.conf

Static IP address templates for dhcpcd.conf

https://www.raspberrypi.org/forums/viewtopic.php?t=140252

######################################################
# TEMPLATE: A static IP address only when no DHCP
#
#           The profile name is arbitrary. Use "fred"
#           if you want. Not much we can put as
#           default servers, but set them up as
#           you usually would.
######################################################
interface eth0
fallback nodhcp

profile nodhcp
static ip_address=10.0.0.1/8
static routers=10.0.0.1
static domain_name_servers=10.0.0.1

Trying to do this

https://www.diyhobi.com/share-raspberry-pi-wifi-internet-ethernet/

Future of Genomics: 10 bold predictions

 Curious about research priorities and opportunities for human genomics for the next decade? You should read on.

The National Human Genome Research Institute (NHGRI) this week published its “Strategic vision for improving human health at The Forefront of Genomics” in the journal Nature.

The strategic vision culminates with 10 bold predictions for human genomics by 2030. Crafted to be both inspirational and aspirational, the predictions are intended to provoke thoughtful discussions (and even debate) about what might be possible in the coming decade.

I must say that I expected people to store their encrypted genome sequences on smartphones anduse 5G networks to launch on the fly analyses a few years back. Not sure if we will have that by 2030!

it's also a good time to review the 5 years prediction from 2015
 Read about gold genomes and platinum genomes... 

 
The 2020 NHGRI Strategic Vision is available online at genome.gov/2020SV.

 

 

 

FAAH-OUT This woman feels no pain!

"A woman in Scotland can feel virtually no pain due to a mutation ...
At age 65, the woman sought treatment for an issue with her hip, which turned out to involve severe joint degeneration despite her experiencing no pain. At age 66, she underwent surgery on her hand, which is normally very painful, and yet she reported no pain after the surgery. Her pain insensitivity was diagnosed by Dr Devjit Srivastava, Consultant in Anaesthesia and Pain Medicine at an NHS hospital in the north of Scotland and co-lead author of the paper....
which the researchers have described for the first time and dubbed FAAH-OUT. "
https://www.sciencedaily.com/releases/2019/03/190327203450.htm

Journal Reference:

    Abdella M. Habib, Andrei L. Okorokov, Matthew N. Hill, Jose T. Bras, Man-Cheung Lee, Shengnan Li, Samuel J. Gossage, Marie van Drimmelen, Maria Morena, Henry Houlden, Juan D. Ramirez, David L.H. Bennett, Devjit Srivastava, James J. Cox. Microdeletion in a pseudogene identified in a patient with high anandamide concentrations and pain insensitivity. British Journal of Anaesthesia, 2019; DOI: 10.1016/j.bja.2019.02.019

1-liner bash to rename spaces in filenames or folder names

Source: https://stackoverflow.com/questions/2709458/how-to-replace-spaces-in-file-names-using-a-bash-script
#non-recursive method

for f in *\ *; do mv "$f" "${f// /_}"; done

HDD clean up; Does it spark joy?

size:gigantic
in Windows Explorer to look for > 128 Mb sized files

Koala Genome assembled on AWS

Excerpted from AWS blog 
 
Five years ago, a research team led by Dr. Rebecca Johnson (Director of the Australian Museum Research Institute) set out to learn more about koala populations, genetics, and diseases. As a biologically unique animal with a limited appetite, maintaining a healthy and genetically diverse population are both key elements of any conservation plan. In addition to characterizing the genetic diversity of koala populations, the team wanted to strengthen Australia’s ability to lead large-scale genome sequencing projects.
Inside the Koala Genome
Last month the team published their results in Nature Genetics. Their paper (Adaptation and Conservation Insights from the Koala Genome) identifies the genomic basis for the koala’s unique biology. 

This work was performed on AWS. The research team used cfnCluster to create multiple clusters, each with 500 to 1000 vCPUs, and running Falcon from Pacific Biosciences. All in all, the team used 3 million EC2 core hours, most of which were EC2 Spot Instances.