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We've been exploring the new #T2T human genome assembly compared to previous versions (our news and views article is out today, link below). Some observations:
(1) Its pretty amazing what the human genome project was able to do in 2004: large-scale gene order is totally conserved
(1) Its pretty amazing what the human genome project was able to do in 2004: large-scale gene order is totally conserved
(2) Some of the chromosomes are nearly identical between the 2013 GRCh38 assembly and T2T. For example, here is a zoom in on Chr10 - just a few gaps in the pericentromere that were filled in with tandem repeats in T2T.
(3) But other chromosomes have been dramatically improved. For example, here are Chr9 and acrocentric Chr14.
Plot legend: sliding window proportion of sequence in genes (dark orange = exons) and repeats (light blue = #repeatMasker, dark blue = #trf); red segments = GRCh38 gaps.
Plot legend: sliding window proportion of sequence in genes (dark orange = exons) and repeats (light blue = #repeatMasker, dark blue = #trf); red segments = GRCh38 gaps.
More good news! Our paper describing DiMeLo-seq is now published in @naturemethods. DiMeLo-seq uses long-read sequencing to map specific protein-DNA interaction sites on single chromatin fibers, with lots of cool applications in epigenomics. 👇 nature.com/articles/s4159… /1
For a general overview, see our previous thread on the preprint (with accompanying Enrique Iglesias references):
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Since the preprint, we further improved the protocol, increasing methylation efficiency 50-60% without sacrificing specificity, and we showed that we can detect mA deposited in vivo by direct fusion of the target protein to a MTase (as in DamID/MadID) doi.org/10.17504/proto… /3
Scientists in the Telomere-to-Telomere (#T2T) consortium have published the first complete, gapless human genome sequence. This can lead to a better understanding of our genomic variations and provide insight for missing heritability and human disease. genome.gov/T2T
Scientists from all over the world worked to complete the project, including many early-career researchers and trainees! Some of these incredible researchers include:
@HHMINEWS @UCBerkeley @epitopic @roneilllab @uconnresearch @UCDavisNews @ucsc @ucscgenomics @UK_Muenster
@HHMINEWS @UCBerkeley @epitopic @roneilllab @uconnresearch @UCDavisNews @ucsc @ucscgenomics @UK_Muenster
Wow! Amazing to hear the updates on the #T2T human genome assembly! Sequence for the acrocentric chromosomes, 5 new chr arms encompassing 66.1 Mb of sequence & 1,561 genes #ASHG21
@aphillippy: Planning to maintain GRCh38 and CHM13 as parallel assemblies. Will build up resources for CHM13 but cannot throw away hg38. If interested in 8% extra genomic sequencing should align and assemble using CHM13. Goal to do #T2T Pangenome. #ASHG21
Nicolas Altemose: 2021 not only anniversary of the human genome reference but 60th anniversary of satellite DNA. #ASHG21
When Human Genome Project researchers announced they had successfully completed sequencing the human genome, it was only about 92% complete. There were still hundreds of gaps or missing DNA sequences. Why was it so difficult to complete the sequence? Let’s break it down! #T2T
A quick refresher: DNA strands are made up of chemical units called nucleotide bases. These are adenine (A),cytosine (C), guanine (G) and thymine (T). Your body reads the order of these letters to determine the info in the strand, just as you read a word to determine its meaning!
An organism’s complete set of DNA is called its genome. Nearly every single cell in the body contains a copy of exactly 3 billion DNA base pairs that make up the human genome. You read that right — 3 BILLION. In other words, the human genome contains a massive amount of DNA!
We are excited to release a GIAB benchmark for 273 challenging medically relevant genes like SMN1 with @sedlazeck @infoecho and many others, using a hifiasm diploid assembly from @lh3lh3. In the process we identified and corrected false duplication errors in GRCh38 1/n
We use the new benchmark to demonstrate a solution that improves short read accuracy from 8% to 100% in important genes on GRCh38 (CBS, CRYAA, and KCNE1), working with @GenomeRef to mask 5 GRCh38 false duplications on chr21, building on recent results from @chrisamiller et al 2/n
With #T2T we are developing a more comprehensive list of false duplications that cover >1Mbp in GRCh38 so stay tuned for an improved masked GRCh38 soon but an initial masked GRCh38 is under ftp-trace.ncbi.nlm.nih.gov/ReferenceSampl…. The #T2T reference from @aphillippy @khmiga fixes these as well!
The #T2T Consortium is excited to release a series of preprints in the coming weeks that describe the assembly and analysis of the first truly complete human genome! 🎉 I will append the papers as they appear to this 🧵, and you can find all our data here: github.com/marbl/CHM13
First things first, a massive high five to my #T2T co-chairs @khmiga and Evan Eichler who shared this vision with me from the start and from whom I've learned so much, as well as the entire #T2T team 🙌 I can't imagine a better group of people! Sorry I can't fit everyone!
"The complete sequence of a human genome" led by @sergeynurk @sergekoren @ArangRhie @MikkoRautiaine3 describes the assembly and initial analysis. We have revealed ~200 Mbp of new sequence, thousands of potentially new genes, and 5 full chromosome arms! biorxiv.org/cgi/content/sh…
