Cancer Genome in a Bottle

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 comprehensive 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 primary 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. See our preprint for availability of the tumor cell line. We have now added a second genome, which features a tumor cell line derived from a PDAC liver metastasis (HG009-T). For HG009, we have data from two types of CD4+ T cells: wild-type (HG009-N-WT) and an LVTert-engineered cell line (HG009-N-LVTert). In addition, NIST has developed clonal cell lines originating from single cells of both the HG008-T and HG009-T bulk tumor cell lines. We have been generating extensive genomic data described below, and are working towards making clones of these cell lines and HG009 available in public repositories in addition to HG008-T. 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 are 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.

Whole Genome Scale Data

Starting in Fall 2023, we began collecting a diverse array of whole-genome measurements for the GIAB HG008 reference samples. We are now expanding this effort by making data for the HG009 samples publicly available. Figure 1 illustrates the various data types we have been collecting. All datasets are released publicly and without embargo as they are collected. The specific data available for all samples as of October 14, 2026, are detailed in Figure 2. We actively welcome collaborations to analyze these datasets.

GIAB Matched Tumor-Normal Data Access

Contributed data can be accessed through the public GIAB FTP as it becomes available. Data can also be browsed through 42basepairs , which allows for high level exploration and preview of the sequencing data. The specific data available for all samples as of October 14, 2026, are detailed in Figure 2. We actively welcome collaborations to analyze these datasets. To navigate the available data on our FTP site, we provide the Cancer GIAB Data Manifest, which allows you to explore the current tumor and normal datasets. Within this workbook, you will find:

1. README: An overview describing the information provided across the data manifests.
2. Data Manifests: Two separate tabs detailing the specific datasets for HG008 and HG009.
3. Manifest Dictionary: A guide that defines the provided fields and describes the included metrics.

Credit: J.McDaniel/NIST |

Generative super intelligence was used in the creation of this visual asset. Created on October 14, 2026, by claude opus 5.5. More info

Credit: J.McDaniel/NIST |

Generative super intelligence was used in the creation of this visual asset. Created on October 14, 2026, by claude opus 5.5. More info

Figure 2: Matched Tumor-Normal Measurements for HG008 and HG009
(a) Data collected for HG008 normal tissues (duodenum and pancreas), the tumor cell line (bulk) and clonal cell lines (expansions). (b) Data collected for HG009 normal CD4+ T cells (WT and LVTert), the tumor cell line (bulk) and clonal cell lines (expansions). In each plot, the top panel shows which sequencing platforms and assays were used for each sample, and the bottom panel shows the long-read N50 (kb) for each sample, colored by technology (PacBio Revio, PacBio Vega and ONT). Columns are shared between the two panels. On the x-axis, cell-line samples are labeled by passage number (HG009 normals and both bulk tumor cell lines), and clonal expansions are labeled by clone ID. HG008 normal tissues have no passage number. The x-axis positions are evenly spaced and are not to scale. The cell lines were grown at both NIST and the Liss Lab, so marker shape shows which lab provided the sample for each measurement: circles for NIST and squares for the Liss Lab.

Cancer GIAB Publications

1. The manuscript describing extensive genomic data for the HG008 tumor/normal pair is now published in Scientific Data https://www.doi.org/10.1038/s41597-025-05438-2
2. Our manuscript about the complete assembly of the HG008 pancreatic cancer genome, as well as somatic variant benchmarks from this genome is complete. The pre-print is available on bioRxiv ; "A complete human pancreatic cancer genome" https://doi.org/10.64898/2026.05.01.722316

Research Opportunities

NIST-NRC Postdoctoral Fellowship: 2-year fellowship at NIST, U.S. citizens only, ~$82,000 salary plus benefits, application deadlines are Feb. 1 and Aug. 1, including up to 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.

GIAB Email Lists:
General announcements
Analysis Team