DRAGEN Array v1.2.0 Release Notes

RELEASE DATE

February 2025

RELEASE HIGHLIGHTS

• Whole-genome copy number and loss of heterozygosity (LOH) calling, with VCF output format, for any human genotyping array.

• B-allele frequency bedgraph output file to power informative CNV visualizations.

• Additional outputs including ISCN and cytoband nomenclature to support cytogenetics applications.

NEW FEATURES IN DETAIL

• Cytogenetics Calling and VCF Output

  • Ability to obtain output files for any human genotyping array. Detection abilities vary by array probe density and spacing.

  • Detects copy number up to 4+.

  • Provides Phred scaled quality score to assess the event quality.

  • Addition of mosaic tagging to detect mosaic deletions and duplications.

  • Three arrays tested for performance including:

    • Infinium Global Diversity Array with Cytogenetics-8

    • Infinium Global Screening Array with Cytogenetics-24

    • Infinium CytoSNP-850K BeadChip using the iScan System

  • Ability to adjust minimum size and probe number for copy number and LOH event calling

• BAF and LRR Bedgraph files

  • Additional bedgraph file output for B-allele frequency (BAF) for use in visualization. Updated file extensions to differentiate BAF.bedgraph and LRR.bedgraph files.

  • Added a smoothing parameter to the genotype gtc-to-bedgraph command for LRR.bedgraph (log R ratio bedgraph file) generation for improved visualization.

  • Bedgraph files are compatible with IGV (Integrative Genomics Viewer) for visualization purposes.

• Cytogenetic annotation and JSON Output

  • Provides summary statistics per sample and per CNV/LOH event. Includes gene count and gene names within each event based on the RefSeq database.

  • Annotates each event using International System for Human Cytogenomic Nomenclature (ISCN) 2020 and cytoband nomenclature based on Ensembl database.

• Pharmacogenomics

  • Added root command pgx for grouping PGx copy number and star allele calling.

  • Fixed issue causing pgx star-allele annotate command to fail mid-analysis when a particular allele is unknown (e.g. from CYP2E1), an issue introduced in version 1.1.

• Added compatibility with new license server (license.dragen.illumina.com) for local star-allele calling.

KNOWN ISSUES

• Some multi-nucleotide variant (MNV) designs reverse complement the "Allele1/2 Top" fields in the Final Report

• Corrupt or invalid GTC files will abort with an error instead of skipping. The corrupt or invalid GTC files will need to be removed before proceeding.

• GTC files do not support non-ASCII characters. This is especially problematic when running DRAGEN Array local if operating system locale settings are not English-based (e.g., en-US) as internal datetime fields could write non-ASCII characters. This will result in the following error:

fail:  ArrayAnalysis.CLI.App[0] 
        [07:17:07 6620]: System.IO.EndOfStreamException: Unable to read beyond the end of the stream. 
             at System.IO.BinaryReader.ReadString() 
             at ArrayAnalysis.Core.GtcFileLoader..ctor(String filePath) in /src/ArrayAnalysis.Core/GtcFileLoader.cs:line 161 
             at ArrayAnalysis.Services.GtcFactory.CreateGtcFromSample(Sample sample, Boolean log) 
             at ArrayAnalysis.Services.GtcToVcfService.Run(GtcToVcfInput input) 
             at ArrayAnalysis.CLI.App.RunCliServiceAndReturnExitCode(BaseOptions opts) in /src/ArrayAnalysis.CLI/App.cs:line 110

There is a workaround to disable globalization and produce valid GTC files:

1. Locate the dragena.runtimeconfig.json file inside the installation directory of DRAGEN Array (i.e., where the .zip or .tar.gz file was downloaded and unzipped).

2. Add the key System.Globalization.Invariant to that file and set its value to true. (i.e., step #2 here: https://github.com/dotnet/corefx/blob/master/Documentation/architecture/globalization-invariant-mode.md#enabling-the-invariant-mode)

3. Re-generate the GTC using the genotype call subcommand.

• SNV and indel variants are always treated as separate variants and are not collapsed in gtc-to-vcf even if they are designed to the same locus.

• Some indel variants are missing from SNV VCF due to mapping issue between the designed indels and the reference genome.

• In the gtc-to-vcf subcommand a mismatch between BPM and CSV manifests will not cause the command to abort with an error. The mismatch will need to be addressed before proceeding.

• During locus combination logic for gtc-to-vcf, duplicate INDELS with HET calls on opposite strands (i.e., probe calls of D/I + I/D) incorrectly report a no call (./.) in the VCF instead of HET (0/1).

• If a sample's sex estimate is called as unknown in the genotyping module, the cytogenetic caller will assume the sample is male. Consequently, detection results on sex chromosomes could be inaccurate if the sample is actually female.

• ISCN annotations in the cytogenetic annotation JSON output file are only provided for variants greater than 1 kb in length. This is often cited as a minimum size limit used to define copy number variants.

• ISCN annotations are not provided for LOH variants in the cytogenetic annotation JSON output file.

• Centromere regions typically have low sequence complexity and are prone to artifacts. As a result, cytogenetic calling results in these regions are likely to be false positives.

• The cyto annotate subcommand produces extraneous logs (e.g., No credential is provided) that can be safely ignored.

• During cyto call, there is a log for the CytoPlatform currently hardcoded to LCG regardless of the product used. This has no bearing on the underlying algorithm and is just what is reported in the log. It can be safely ignored.

• A non-default value of the --smoothing parameter for the genotype gtc-to-bedgraph command triggers a bug causing wrong values in the LogR Ratios (LRR) bedgraph. It is advised users use the default (0), which produces a valid LRR bedgraph with raw signal for visualization purposes. The --smoothing parameter will be disabled in next release of DRAGEN Array.

• The cyto call command may throw an overflow error in very rare cases when no variants are detected in noisy or low-quality samples. Contact [email protected] if you encounter this issue.

• The minimum deletion/LOH/duplication thresholds shown in the cyto annotation JSON may be shown in the wrong units when set higher than the cyto calling thresholds.

• Cyto CNV/LOH variants with quality scores of 0 seen in the cyto call VCF files cannot be passed into the annotation output json files.

• CYP2A6 *1 definition incorrectly includes NC_000019.10:g.40848264_40848265delinsT.

• DRAGEN Array – Cytogenetics Calling and DRAGEN Array - Cytogenetics analysis + Emedgene interpretation cloud analyses may fail around 200 samples in one batch due to high memory usage. Recommended workaround is to run smaller batches.

• Sample with a reference allele for ABCG2 genes will have missing phenotype annotations when running the command pgx star-allele annotate.

• Rare intermittent memory issues during star allele calling. Example error message: The model has been changed since the solution was last computed.. To work around the issue, the user should restart star allele calling or run it on a machine with more memory.

• Some simple variants have REF and ALT delimited by _ instead of > in the star_alleles.csv and metabolizer status JSON files (e.g., "ryr1.38577931a_c" instead of "ryr1.38577931a>c")

• Occasional star-allele solution score discordance between Linux and Windows OS with concordant solution ranking.

KNOWN LIMITATIONS

• Genotyping only supports diploid organisms. Polyploid genotyping is currently not supported.

• DRAGEN Array Cytogenetics analysis is intended for constitutional samples only, oncology samples not supported at this time.

• DRAGEN Array Cytogenetics analysis was only validated for specific array platforms (Infinium Global Diversity Array with Cytogenetics-8, Infinium Global Screening Array with Cytogenetics-24, Infinium CytoSNP-850K BeadChip using the iScan System).

• DRAGEN Array Cytogenetics analysis may call large events that are broken into smaller pieces and require visual confirmation.

• DRAGEN Array Cytogenetics analysis does not produce mosaic fraction estimation or mosaic ISCN notation at this time.

• When using CytoSNP-850Kv1-4_iScan_B, GSACyto-24v1_20044998_C, or GDACyto-8v1-0_20047166_E manifests, DRAGEN Array Cytogenetics analysis will be unable to call events or visualize probes in the PAR (pseudo-autosomal regions). Please reach out to [email protected] for additional details.

• GT is hardcoded to homozygous alt (1/1) for cyto VCF entries.

• IDATs originating from NextSeq550 not tested.

• Star allele calling does not support novel alleles; only alleles defined in the PharmVar and PharmGKB databases are supported.

• CYP2D6 non-*36 star alleles with exon 9 conversion, such as *83, are reported as *36 with *83 as an underlying allele.

• Command line options unsquash-duplicates and filter-loci for gtc-to-vcf conversion should not be used when star allele calling is desired. In addition, VCFs must be gzipped and tabix indexed (the default for gtc-to-vcf) to be used in star allele calling.