New GIAB resources, preprints, and posters at ASHG

[Zook, Justin M. (Fed)]

Dear Genome in a Bottle,

 

We are excited to have released several new GIAB products in advance of ASHG, including v1.0 benchmarks for tandem repeats and X&Y chromosomes, a new corrected GRCh38 reference, new stratifications for T2T-CHM13, new RNA sequencing and tumor/normal data, and a v1.0 T2T-HG002 assembly with the T2T Consortium!

 

We have updated the GIAB webpage with the following information:

1. v1.0 TR benchmark for HG002 indels and SVs >=5bp in tandem repeats on GRCh38 (preprint, and ASHG poster PB4495 that also includes the XY benchmark and T2T “Q100” work below)
2. v1.0 XY benchmark for HG002 small variants in chromosomes X and Y on GRCh38 (preprint)
3. GIAB v3 GRCh38 reference with masked false duplications and contaminations, as well as decoy sequences from CHM13, which we are now using for GIAB analyses (refinement of reference from https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02863-7). 
4. v3.3 stratifications, including refinements to GRCh37 and GRCh38 (e.g., separate A/T and G/C homopolymer beds) as well as new stratifications for T2T-CHM13v2.0 (preprint, and ASHG poster PB3519 about new results for modeling sequencing errors)
5. New RNA sequencing data for the HG002 LCL and iPSCs, and HG004 and HG005 LCLs, including Illumina, PacBio Iso-seq and MAS-seq, and ONT direct RNA and cDNA
6. New Tumor/Normal WGS for large batch of the HG008-T pancreatic tumor cell line, including Illumina WGS, ONT WGS, Bionano, and low pass Bioskryb single cell WGS, with more data on tumor and normal in process. (see data manifest in new Cancer GIAB website and poster PB5090 at ASHG)
7. v1.0 T2T-HG002 Assembly in collaboration with Nancy Hansen, Adam Phillippy, and many others in the T2T Consortium, which we will be using to make new GIAB benchmarks. We have uploaded preliminary draft small variant and SV benchmarks from v0.9.

 

Thanks to many of you who have contributed to this work, and look forward to seeing many of you at ASHG this week!

 

Justin, on behalf of the GIAB team

 

 

[Zook, Justin M. (Fed)]

Dear Genome in a Bottle,

 

It was great seeing many of you at ASHG! For those who weren’t able to attend or are interested in taking another look at our posters about new GIAB benchmarks, tumor/normal data, and modeling variant errors, I’ve uploaded them at https://www.slideshare.net/GenomeInABottle/documents.

 

Let us know if you have any questions, and thanks to many of you for contributing to this work!

Justin

[Zook, Justin M. (Fed)]

Dear Genome in a Bottle,

 

Sorry for the late reminder, but we will be having our GIAB analysis team call on Monday, Nov 13, at 1pm EST, where we’ll give an update on data and plans for the tumor/normal as well as briefly describing the other new resources announced in the emails below. We will plan to record for those who cannot make it

 

Connection information is:

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Meeting number (access code): 2764 901 8890

 

Meeting password: gsMhgGm@375

 

 

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Cheers,

Justin

 

From: 'Zook, Justin M. (Fed)' via GIAB Analysis Team <giab-anal...@googlegroups.com>
Date: Monday, November 6, 2023 at 12:21 PM
To: genome-in...@googlegroups.com <genome-in...@googlegroups.com>, GIAB Analysis Team <giab-anal...@googlegroups.com>
Subject: [giab-analysis-team] Re: New GIAB resources, preprints, and posters at ASHG

Dear Genome in a Bottle,

 

It was great seeing many of you at ASHG! For those who weren’t able to attend or are interested in taking another look at our posters about new GIAB benchmarks, tumor/normal data, and modeling variant errors, I’ve uploaded them at https://www.slideshare.net/GenomeInABottle/documents.

 

Let us know if you have any questions, and thanks to many of you for contributing to this work!

Justin

 

From: Zook, Justin M. (Fed) <justi...@nist.gov>
Date: Wednesday, November 1, 2023 at 1:07 PM
To: genome-in...@googlegroups.com <genome-in...@googlegroups.com>, GIAB Analysis Team <giab-anal...@googlegroups.com>
Subject: New GIAB resources, preprints, and posters at ASHG

Dear Genome in a Bottle,

 

We are excited to have released several new GIAB products in advance of ASHG, including v1.0 benchmarks for tandem repeats and X&Y chromosomes, a new corrected GRCh38 reference, new stratifications for T2T-CHM13, new RNA sequencing and tumor/normal data, and a v1.0 T2T-HG002 assembly with the T2T Consortium!

 

We have updated the GIAB webpage with the following information:

1. v1.0 TR benchmark for HG002 indels and SVs >=5bp in tandem repeats on GRCh38 (preprint, and ASHG poster PB4495 that also includes the XY benchmark and T2T “Q100” work below)
2. v1.0 XY benchmark for HG002 small variants in chromosomes X and Y on GRCh38 (preprint)
3. GIAB v3 GRCh38 reference with masked false duplications and contaminations, as well as decoy sequences from CHM13, which we are now using for GIAB analyses (refinement of reference from https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02863-7). 
4. v3.3 stratifications, including refinements to GRCh37 and GRCh38 (e.g., separate A/T and G/C homopolymer beds) as well as new stratifications for T2T-CHM13v2.0 (preprint, and ASHG poster PB3519 about new results for modeling sequencing errors)
5. New RNA sequencing data for the HG002 LCL and iPSCs, and HG004 and HG005 LCLs, including Illumina, PacBio Iso-seq and MAS-seq, and ONT direct RNA and cDNA
6. New Tumor/Normal WGS for large batch of the HG008-T pancreatic tumor cell line, including Illumina WGS, ONT WGS, Bionano, and low pass Bioskryb single cell WGS, with more data on tumor and normal in process. (see data manifest in new Cancer GIAB website and poster PB5090 at ASHG)
7. v1.0 T2T-HG002 Assembly in collaboration with Nancy Hansen, Adam Phillippy, and many others in the T2T Consortium, which we will be using to make new GIAB benchmarks. We have uploaded preliminary draft small variant and SV benchmarks from v0.9.

 

Thanks to many of you who have contributed to this work, and look forward to seeing many of you at ASHG this week!

 

Justin, on behalf of the GIAB team

 

 

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[Zook, Justin M. (Fed)]

Dear GIAB,

 

I’ve included links to the slides and recording below, and please let us know if you have any feedback or are interested in helping to create benchmarks for somatic small variants, SVs, and/or CNVs from the new HG008-T data (see data manifest in new Cancer GIAB website).

Slides: https://docs.google.com/presentation/d/1BQDjE2lfrKGYDWUrXCVqD48bvFsqKmGgXOYcWSpHRqM/edit?usp=sharing

Recording: https://drive.google.com/file/d/1W6rlfZSi9exsetdgM-b8ur-ZUaYcailz/view?usp=drive_link

 

Cheers,

Justin

[Zook, Justin M. (Fed)]

Dear Genome in a Bottle,

 

We will be having our GIAB analysis team call on Monday, Dec 11, at 1pm EST, where Bob Schnabel, Jenna Kalleberg, and Brenda Murdoch will be joining us to discuss their proposed “GIAB-Ag” project to develop GIAB-like resources for cattle and potentially other agricultural animals. We’ll also give an update on data and plans for the tumor/normal, including a discussion about sequencing options for the cells we have saved from different passages of HG008.