Colorectal cancer rates in adults under 50 have doubled since the late 1980s. One in five colorectal cancer diagnoses now occurs in someone under 55, up from one in ten in 1995. A new study highlights the most concrete factor responsible for this trend. Using DNA methylation profiles as molecular records of lifetime exposure, the authors compared cancer patients under 50 with patients over 70 and identified the herbicide picloram as a significant new risk factor. There are converging lines of evidence. The picloram exposure signature was significantly elevated in early-onset tumor tissue and replicated across nine independent patient cohorts. Across 21 years of US county-level data spanning seven states, higher picloram use tracked higher early-onset CRC incidence, and the signal held after adjusting for income, education, and the use of other pesticides. Picloram associated tumors also showed a distinct molecular profile, with APC mutations at 74% versus 90% in low-exposure tumors, suggesting these cancers follow a different biological pathway than classical CRC. Picloram entered commercial use in 1964. Patients now diagnosed in their 70s were already adults before meaningful exposure was possible. Patients now diagnosed in their 30s and 40s were exposed across childhood and adolescence, the developmental windows when epigenetic programming is most plastic. This study delivers the first triangulation of molecular, ecological, and temporal evidence pointing at a specific environmental driver of one of the steepest cancer trends in modern epidemiology.

RT @EricTopol: Getting your real-time heart rhythm monitored for 10 days now requires an ECG technician to review and notify your doctor of…

MEM-based pangenome indexing for k-mer queries biorxiv.org/cgi/content/shor… #biorxiv_bioinfo

I'm a big fan of @sentieon's applications for analyzing genomics data. Read this post about cost-effective and accurate genomics analysis with Sentieon on AWS aws.amazon.com/blogs/hpc/cos… via @awscloud

30x WGS data processing using Intel, AMD, and ARM instances on the Oracle Cloud with the Sentieon software. <$1 in On-Demand costs with ARM instances. blogs.oracle.com/cloud-infra…

Happy to see these updated benchmark results! DNAscope will output some non-pass variant candidates with a FILTER field set. @holtjma's earlier benchmark considered all variants, causing DNAscope to have a high recall but low precision. The new results are more balanced.

Looking in variant calling accuracy comparison in the long read space. #genomics #bioinformatics #machinelearning #longread great team work speared ahead by @YihChii and @Chai_Arkarachai in @dnanexus medium.com/@YihChii/f6efec6b…

I am looking for a talented programmer to join our team working on algorithms and software for multiple aspects of genomics data analysis. Grant funded; flexibility with a competitive salary and benefits. Experience with C or Rust required. Please share. utah.peopleadmin.com/posting…

Fun collaborative paper that includes a new @GenomeInABottle @NIST benchmark that helps demonstrate up to 12x reduction in errors on the #T2T reference genome for challenging medically relevant genes. Lots of other improvements over GRCh38 as well! biorxiv.org/content/10.1101/…

We are releasing Clair3 at github.com/HKU-BAL/Clair3. Clair3 is a small variant caller for long-reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2 HG004), and a better Indel F1-score, while ... 1/

AnVIL Project Manager opening in the @mike_schatz lab at @JohnsHopkins jobs.jhu.edu/job/Baltimore-A… @useAnVIL #UseGalaxy

Please RT: My group has a #Bioinformatics #postdoc #job available: jobs.bcm.edu/job/Houston-Pos… Come join us to develop new methods and expand our knowledge about Structural Variations together @BCM_HGSC. #Computational #postdoctoral #BigData #analytics #python #fellowships #Genomics

I knew it.

The Telomere-to-Telomere consortium is proud to announce our v1.0 release of a complete human genome. When @khmiga asked me to team up on this a few years ago, I wasn't sure it would be possible. Now down to just 5 gaps. What a journey! Read more here genomeinformatics.github.io/…

Nice article in Bio-IT World about the @precisionfda challenge using the new @NIST @GenomeInABottle benchmark described in doi.org/10.1101/2020.07.24.2… bio-itworld.com/2020/09/02/t…

Home office mood

Awesome job by the @sentieon team.

I am excited that the @GenomeInABottle Structural Variation (SV) paper is out today in @NatureBiotech rdcu.be/b4UMa. Characterization of 12,745 SV as a gold standard. A huge #milestone for the detection of SV highlighting the challenges opportunities that remain

For those who are interested in research-based solutions to stop police violence, here’s what you need to know - based on the facts and data. A thread. (1/x)

Proud to announce our new manuscript from the @hilsomartin & @mehurles groups @sangerinstitute. We did a deep dive into the relationship between rare variant burden and reproductive success with the amazing data from @uk_biobank! biorxiv.org/content/10.1101/… Tweet summary 👇