Cancer Genome in a Bottle

Summary

Part of the Genome in a Bottle Consortium hosted by NIST dedicated to authoritative characterization of benchmark cancer genomes. Complements NIST's current DNA copy number Reference Materials for HER2, as well as EGFR and MET.  Sign up for General GIAB and Analysis Team email lists.

Interested in job opportunities or collaborations with us? Contact justin.zook [at] nist.gov (Justin Zook).
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Description

Goals:

This project is an extension of the Genome in a Bottle Consortium to develop the technical infrastructure (reference standards, reference methods, and reference data) to enable translation of cancer genome sequencing to clinical practice and innovations in technologies. The priority of GIAB is authoritative characterization of human genomes for use in benchmarking, including analytical validation and technology development, optimization, and demonstration.

Reference Samples:

NIST has been collaborating with Andrew Liss at MGH to develop new tumor cell lines with paired normal samples that are explicitly consented for fully public dissemination of genomic data and cell lines. The first tumor cell line (HG008-T) is from a pancreatic ductal adenocarcinoma, for which we have paired normal pancreatic (HG008-N-P) and duodenal tissue (HG008-N-D) for sequencing, but no normal cell line. We currently are collecting extensive genomic data described below, and are working towards making these cell lines available in public repositories. We plan to have another pancreatic tumor cell line with a paired normal cell line in the near future, but these are still under development. We also welcome additional collaborations for tumor and normal cell line pairs that are explicitly consented for fully public dissemination of genomic data and cell lines.

Benchmark (or "High-confidence") Variant Calls and Regions:

We will be working with the GIAB community to develop benchmark variants for the tumor and normal samples, using assembly-based and mapping-based approaches. We welcome collaborations in this new project.

Sequencing Data:

Starting in the Fall 2023, we began collecting  diverse long and short read paired tumor and normal sequencing data for GIAB HG008 samples. We are making the data public, without embargo, as we collect them.  The data being collected is described in Table 1 (long range) and Table 2 (short range).   We welcome collaborations to analyze these data. 

Data Access:

These contributed data can be accessed through the public GIAB FTP as it becomes available.  We further provide  the Cancer GIAB Data Manifest  which allows for exploration of the tumor and normal data currently available on the FTP.  If you are interested in exploring the manifest, you can create a filter view by 1) selecting the entire spreadsheet 2) Data → filter views → create new filter view.  Please note tumor data collected from year 1 (2022) is from a prior passage of tumor cells and is emphasized in RED.  All current tumor data being collected, is from a large batch of tumor cells known as 0823p23.  Please take these passages into consideration when choosing tumor datasets you are interested in exploring. 

Table 1:  Long Range Datasets
Pending and available long range datasets for HG008 tumor and normal samples. Datasets that are available have been QC'd and are noted by estimated coverage and read lengths.  Coverage estimates reflect the expected coverage of diploid regions of the normal and tumor samples, assuming no whole genome duplication has occurred. If there are multiple dataset available those will be denoted by "(dataset #)" next to stats. See the GIAB FTP or data manifest linked above for access to the available data.  This table is updated as data are received, last update 2024-03-27.

Estimated Read Lengths	Technology	HG008 tumor cell line (T) 2022 passages	HG008 tumor cell line (T) large batch 0823p23	HG008 normal duodenal tissue (N-D)	HG008 normal pancreatic tissue (N-P)
~100 - 300 kb	Oxford Nanopore Technologies (UL)	NA	~54X , N50 127kb	pending	pending
~10 - 100 kb	Oxford Nanopore Technologies (duplex)	NA	pending	pending	pending
~35 kb	Oxford Nanopore Technologies (std)	NA	~63X , N50 35kb	pending	pending
~10 - 20 kb	PacBio HiFi (Revio)	NA	~116X, N50 18kb	pending	~35X, N50 17kb
150 kb - multi Mb	Bionano Optical Mapping	NA	available	NA	NA
2x150 bp	Arima and Phase Genomics HiC-Illumina	Phase Genomics available	Arima in QC	Arima in QC	NA
chromosomal	Karyologic karyotyping	available	NA	NA	NA

Table 2:  Short Range Datasets
Pending and available short range datasets for HG008 tumor and normal samples. Datasets that are available have been QC'd and are noted by estimated coverage and read lengths.  Coverage estimates reflect the expected coverage of diploid regions of the normal and tumor samples, assuming no whole genome duplication has occurred.  If there are multiple dataset available those will be denoted by "(dataset #)" next to stats.See the GIAB FTP or data manifest linked above for access to the available data.   This table is updated as data are received, last update 2024-03-27.

Estimated Read Lengths	Technology	HG008 tumor cell line (T) 2022 passages	HG008 tumor cell line (T) large batch 0823p23	HG008 normal duodenal tissue (N-D)	HG008 normal pancreatic tissue (N-P)
2x150 bp	Illumina WGS	(1) ~191X , 2x150bp (2) NA	(1) in QC  (2) ~100X , 2x150bp (in final QC)	(1) in QC  (2) ~100X , 2x150bp (in final QC)	(1) ~150X, 2x150bp  (2) NA
150 bp	Element - AVITI - short insert - (~350 bp)	NA	~87X, 2x150bp	61X, 2x150bp	NA
150 bp	Element- AVITI - long insert (1000+ bp)	NA	pending	pending	NA
100 - 200 bp	PacBio Onso	NA	pending	pending	NA
~300 bp	Ultima UG100	NA	in QC	in QC	NA
50 bp	BioSkryb single-cell WGS - Illumina	NA	<<1X , 120 cells, 2x50bp	NA	NA
~300 bp	Bioskryb single-cell WGS - Ultima	NA	in QC	NA	NA

Research Opportunities:

NIST-NRC Postdoctoral Fellowship: 2-year fellowship at NIST, U.S. citizens only, ~$75,000 salary plus benefits, relocation expenses included, application deadlines are Feb. 1 and Aug. 1, requires 10 page research proposal. Contact Justin Zook if you are interested in writing a proposal on a genomics research project. We have opportunities posted for metrology in Cancer Genomics, Diploid Assembly, Epigenomics and Transcriptomics, Biological Data Science/Machine Learning, and Precision Medicine.

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